Not defending them at all. Merely pointing out that their presence was the result, as another poster pointed out, of a very different history than America's.
The Inquisition was still active and executing people in both Spain and her colonies in the early 19th century. There was, by law, no religious freedom. The death penalty existed and was enforced for heresy. Not unlike the present penalties for apostasy in Muslim countries.
IOW, the Catholicism against which the leftists of Spain and Mexico rebelled was a part of the state, of the oppressive system against which they fought. Far more oppressive than anything in American history. So, while regrettable, it is not surprising that the reaction against a truly oppressive Church was itself much more violent than anything in US history.
It sounds like you're trying to explain away the leftists' actions. Their ideology was going to target the Church and religion in general, regardless of its level of influence.