To be honest, many religions are prone to go astray from their founding principles, at least in those that I know of from inquiry into the subject.
And there seem to be regular attempts at "reformation" as well, common to many religions, Christianity, Judaism and Islam being good examples of such.
And you have to concede that if certain trends become "normative", then that ipso facto defines the religion as a whole.
For example: Some of the things you speak of did "define" the official pronouncements of the powers-that-were in, say, the Roman Catholic Church at the time of Galileo, or the Inquisition. Cardinal Ximenez, for example, was commissioned specifically BY THE POPE HIMSELF, to prosecute the Inquisition, and the "trial" of Galileo took place in the Vatican.
OTOH, the "jihadists" are a fringe group, an outgrowth of (but not necessarily in total concert with) the "Wahhabi" movement in the Suni Muslim faith. Outside of a handful of clerics, considered renegade by the greater body of Islamic clerics, there is no real "authority" for their doing what they have done.
Thus to condemn ALL OF ISLAM for the actions of a comparative few outlaws is simply untenable. It is as if you were to look at the incidents you mention, and decide that "all Christians" want to kill Jews and stifle scientific inquiry.
And you have to concede that if certain trends become 'normative.' then that ipso facto defines the religion as a whole.
For example: Some of the things you speak of did "define" the official pronouncements of the powers-that-were in, say, the Roman Catholic Church at the time of Galileo, or the Inquisition. Cardinal Ximenez, for example, was commissioned specifically BY THE POPE HIMSELF, to prosecute the Inquisition, and the "trial" of Galileo took place in the Vatican.
I think that we should differentiate between religion and church. To me, the former is a system of beliefs, whereas the latter is a social institution promalgating those beliefs. With this distinction in mind, observe how everything falls into place. I would cocede to the following statement: "if certain trends become 'normative,', then that ipso facto defines the church. The above-quoted example you give now works wonders. And it should: we know an entity by its actions, and this is true for a social insitution such as church. As you point out, the actions of the Catholic Church at the time you mention were (i) extensive and consistent, and (ii) authorized from the top. We are justified, therefore, to conclude that they represented the essense of the Church at the time.
Has the Church contraditicted the religion, wavered from it, or was, as it claimed, in line with the teachings? That's the problematic part: we don't really know what the religion actually says. All of the holy books, in all religions, are fairly allegoric. Which gave the Church the "right" to burn Jordano Bruno at the stake and, at the same time, gives us the "right" to disagree with that position. This very vagueness gave Papacy the right to sell indulgences and, at the same time, gave the right to Martin Luther to rebel against that practice as a Christian. In other words, the ambiguities of religion allow the church to contradict itself. That is, to say one thing in one century and something quite opposite in another. All the while promulgating the purpotedly same religion.
You may have seen my other posts, where I argue that we are at war with the "Islamic church" rather than Islam. In complete similarity with your example, the narrowminded support of evil by the Arab sheiks (I always remember that Turks are Muslim too but do not fall into this category) is (i) widespread and consistent, and (ii) goes all the way to the "top," i.e., leading sheiks. Thus, we are justified in saying that it is the essense of the Islamic church today.
We are not, and should not be, at war with Islam the religion. The "Islamic church" of tomorrow may be very different than the one today, just as the Catholic Church does not authorize autodafe any longer. Incidentally, Islamic church in al Andalus, the Moorish Spain, was a model of peaceful coexistence of Islam, Chritians, Jews, and pagans. So the "Islamic church" of yesterday was also different from the one we see today. Needless to say, the religions as represented by the Koran and the Bible, repsectively, remained the same.
Thus, the desinction between the church and the religion itself seems to give a unified and internally consistent view of both the past and the present.
What do you think of this?