First - I agree that prior to the passage of the 14th, the 1st did not apply to the states.
Second - I don't disagree with the fact that worship services have been held in government facilities, nor do I condemn such action.
Third - As you well know, the question of Incorporation is not an easy or one-sided question. There is much evidence on both sides of the issue. The Court didn't make it up out of thin air. I have posted to you quotes from the debate on the 14th indicating that incorporation was the intent. You have posted information on the Blaine amendment which - if taken a certain way - could indicate that incorporation happen with the 14th. I have posted historical information on the intent behind the Blaine Amendment - which was specifically intended to maintain, not eliminate, informal Protestant establishment in the states.
Fourth - one point of disagreement that lingers, from a factual standpoint, is your contention that the courts rejected incorporation prior to Gitlow. The only case you have cited from 1867 to 1925 is Davis v. Beason. Davis v. Beason DOES NOT say that the 1st Amendment does not apply to the states. I am not aware of any case in that time period that does. If you are, I'd love to see it.