No intent was made nor implied that democracy supercedes religion. But you must agree, I'm sure, that throughout history, counties with the strongest religious influence within the government reflected the lowest levels of democracy. A pure democracy is worthless. But a republican form of government that provides democratic ideals for the majority but protects the rights of the minority should be the goal of every country on the globe. Does this mean that religion has no place? Of course not. Does this mean that specific religions have a greater role than any other? Only by the will of the people! Democracy must protect religion, but has no responsibility to preserve it. And more importantly, must not place itself in a position to sponsor or even favor one over the other. While the founding fathers were all religious men, and their religious suffusion most certainly played a role in the founding documents, nonetheless all were aware of the dangers of state sponsored religions and the resulting First Amendment was no accident.
While I have little objection against the spirit in which the American Constitution was written, I think that today's political thinking, especially in Europe, has moved away from constitutionalism of Lockean England and republican America, toward the unfortunate attitude that "if we vote for it, it's gotta be the law". That is no freedom.
Why is that not freedom? If it does not trample on the legitimate rights of others, then it is not unjust and most certainly must reflect freedom from any social definition. A Catholic does not condone birth control or gay union. But is it not freedom to permit those who do condone it to engage in it since it does not infringe on the rights of others?
Indeed it is not always self-evident what the natural law is, while it is always (well, leaving voting irregularities aside) evident what the people voted for. There is no substitute for discernment the will of God, no matter how tempting it is to simply put stuff to a vote.
I don't disagree in principle, but again even within the broad range of Christian sects there will be many differences of opinion of what specifically will constitute God's will. If you add in the other major religions of the world, you will have even greater distinctions. This is the very reason why republican government cannot be a theocracy. They are mutually exclusive.
Some of your examples are off-target. Napoleon had a very strained relationship with the Church, which never really recognized him as a valid monarch (The Pope that was present at his coronation was his prisoner)
But then which period did the Church more favorably recognize: the aristocracy of Louis XVI where people were starving to death, the Jacobin period where the guillotine and insane revolutionaries destroyed all, or the Napoleonic period where imperialism ruled?
The use of gas against combatants is not inherently injust method of war; nor do I set up the First World War as any kind of standard by merely pointing out that remnants of civilized behavior were still apparent then.
I don't know which gas you are referring to, blister agents that create huge blisters over your entire body until infection finally kills you, mustard gas where your lungs are burned beyond use, or nerve gas where death comes with difficulty but at least somewhat quicker than the first two. In WW I, mustard gas was the WMD of choice. When I was a young boy, I met a man who had been a victim of mustard gas in the civilized war. He was constantly drooling from both his nose and his mouth. He was hit with the gas 30 years earlier, and doctors then could do nothing for him.
Regarding the Cathars and other heretics, -- they were considered enemy of the state and were suppressed as such. Insurgencies of no religious significance were put down with equal brutality. The Church could not declare their heresies valid because they were not valid; yet nothing short of that would have spared those who chose not to recant.
Is this any less valid than the persecution of Catholics and other Christians in Muslim countries today...for heresy? Any church of whatever sect or denomination that countenances such brutality for religious beliefs cannot in any way be linked with freedom. This simply points out that the link of the Church to the government destroys the concept of individual rights and freedoms. You defended the Spanish Inquisition by reflecting that it was the State, not the Church that carried out the punishment. You did the same here in this example. But the State would not have done such but for the direct influence of the Church. That history underscores the importance of church-state separation.
Insurgencies of no religious significance were put down with equal brutality.
The brutality notwithstanding, an insurgency against a valid established government must of course be put down, or the government has no legitimacy. Heresy does not qualify as an insurgency against a legitimate government, only against a religious philosophy.
Parenthetically, if gnosticism, with its belief in hidden knowledge accessible to a caste of priests only, and evilhood of all human effort except extreme self-negation, were to gain the upper hand anywhere, men of secularist-humanitarian outlook would have much more than an occasional auto-da-fe to complain about.
If strict separation of church and state is maintained, then gnosticism, paganism or any other religious or pseudo-religious belief is irrelevant. And then the occasional auto-da-fe will be found only in history texts.
Freedom and protection of individual rights are synonymous. So if a political process results in individual right violations, this process does not belong to a free society. If, for example, a society takes a vote on the proposition that every redhead should have his property confiscated, and the majority wins, that is no freedom even though the election was "free".
Exercise of religion is one such right. It includes public acts, -- such as prayers, pageants, and erection of monuments, as well as private acts. The government has an obligation to protect religion in both the public and private sphere, or this government oppresses freedom.
Moreover, religion is a public asset. Not just freedom of conscience, but the entire spiritual and cultural heritage is an asset. The government has an obligation to preserve this asset, just like it has an obligation to preserve mineral or esthetic assets of a country. If religion is impoverished through government decree, then that government committed a theft of public treasure and does not stand for freedom.
Some institutions of free society, -- primarily marriage and educational institutions, -- are built on top of religion and are likewise national assets. A government that drives religion out of the classroom, permits no-fault divorce on demand, or encourages destructive behavior by inventing constructs like gay "marriage", -- is a government guilty of theft.
I understand that minority religions, and irreligion, have rights as well. A healthy society finds ways for dominant culture to co-exist with minority culture, typically, through local self-government. Needless to say, the West has been moving in the exactly opposite direction, toward destruction of dominant religious and cultural heritage and toward centralization around the least common denominator principle.
Heresies of the early Church and of the Middle Ages were insurgencies that threatened the social fabric. They were a close equivalent of threats to secular order that we are familiar today, such as fascism or communism, and we did not hesitate to fight those. Recall that at that time the social fabric was the religious fabric. The anabaptists in Muenster (I think) murdered and drove out everyone who disagreed with them, and confiscated private property. The false converts to Christianity in Spain were a real threat to a country that just went though a religious civil war to drive the Muslim out. This is not to justify every prosecution of every heretic, -- some clearly were abuse of power, but one needs to see those things in their historical perspective.
Separation of church and state has become a code word for destruction of religion in the public space. But when one resists that, the argument immediately goes to the bogeyman of Islamic theocracy. In fact, Christianity in the West scarcely had a period even remotely resembling a monolythical theocracy. The Roman Empire following Constantine managed to peacefully accomodate a pagan majority. The early medieval kings were completely independent from the Church, even those that were Christian. When they insisted on appointing bishops, -- a clear power grab by the secular medieval state, -- the Investiture Controversy ensued and Gregory VII was able to restore balance. When Aquinas defined the separation of church and state by function, -- one cares for the souls, the other for the public good, -- he had nearly a millenium of tension and balance to look at in European historical experience. The Establishment clause in the US Constitution is a late comer to the controversy, did not draw on a comparable breadth of historical experience, and by now has been completely emasciated of all meaning.
The Church had tepid support for the Bourbons as the only legitimate government France had at the time. It most certainly did not recognize the Jacobins that slaughtered clergy by the thousands. Napoleon probably got credit for getting rid of the Jacobins, but his reign was not viewed as legitimate except under duress.
I am sure poison gas can cause a terrible injury, and so can any other weapon. But as long as it is used against combatants, there is no moral reason to single it out for opprobium.