Again historically inaccurate. The 14th Amendment was never intended to apply the establishment clause to the states. That is evidenced by the Blaine Amendment which failed and 14 other attempts to begin the amendment process in Congress applying the 1st Amendment to the states.
The 14th Amendment was intended to protect the individual rights of all US citizens. A worthy cause. The establishment clause was a restraint on the federal government, not an individual right.
Of note here is that all the states managed to disestablish state religions without the omnipotent 14th Amendment and it's penumbras.
But that's neither here nor there. The Constitution never required the banning of religion from the public square. Quite the contrary as evidenced by Article 1 Section 7 of the US Constituion which proscribes doing business on Sunday, a bow to the Fourth Commandment. More to the point the founders acknowledged that rights come from God, "the Creator", not from the state, the SCOTUS or Presidents writing letters to Danbury Baptists.
Banning of religion from the public square is Marxist, not Jeffersonian.
Which brings us to your final paragraph. Undoubtedly in times past there has been lots of killing and mayhem due to religion and there is to this day. But if you want to go purely on a numbers basis Stalin, Mao, Pol Pot et al have religion beat by miles and there deeds have been in the recent past, not ancient history.
You can argue that God shoul be banned from the public square because it offends some folk but you can't do it honestly from a historical or Constitutional basis.
If you want God and religion banned from public you should do it honestly be amending the Constitution to do just that and not rely on judicial activism whne it accords with your ideology. When they come for your guns don't be surprised if they find a right to be free of weapons in the 14th Amendment.
I agree that the 14th Amendment was intended to protect individual rights, but would add that religious freedom (and, more broadly, intellectual freedom) is not only an individual right, but arguably one of the most important individual rights we have. The Founding Fathers, such as Jefferson and Madison, were acutely aware of the long, sorry history of the commingling of church and state during that time that historians now call the Dark and Middle Ages. Indeed, many people came from Old Europe to the New World to escape religious tyranny.
If the State has the right to impose religion on you, then it effectively owns or controls your mind and your life -- the very opposite of the State's recognition of your "inalienable right to life, liberty, and the pursuit of happiness." It is no accident that the man who wrote these words in the Declaration of Independence was also the man who explained that the establishment clause of the First Amendment established the principle of separation of church and state.
I don't think that our choice is between religion and Communism (or Marxism, or socialism), but between freedom and statism -- whether the government recognizes your inalienable right to life, liberty, and the pursuit of happiness, or whether the government violates these rights to some degree by asserting ownership or control over your mind, your property, and your life. Theocracy, or religious tyranny, is merely one form of statism. Communism is another form of statism. Both forms, and many other variations, are to be distinguished from the constitutional republic that our Founding Fathers actually intended for us, a form that -- albeit imperfectly -- was based on the individual rights philosophy outlined in the Declaration of Independence.