Because it wasn't up to him. Nor was the federal Constitution, which he had nothing to do with.
Your problem is that you simply ignore history in order to cling to your leftist delusions. The Bill of Rights was not applied to the states until after the civil war. That does not change the fact that the First amendment does not reach beyond forbidding the establishment of a religion. This was the doctrine extended to the states, not the nonexistent principle of complete non-interference in anything religious, which was never the meaning of the First amendment, and so does not apply to the states either.
You're ignoring the whole reason for the argument in the first place: that religious authority in government, especially held by individual government officials willing to abuse their authority, is a major threat to freedom.