So, in your opinion, there’s a moral equivalence between the two sides?
Well, it’s certainly not a case of brutal government persecuting unresisting Christians as in ancient Rome.
While the government was certainly brutal enough, the Catholics resisted quite effectively, to the point that estimates have considerably more casualties on the federal side than on that of the rebels.
You can call that religious persecution if you like, but it looks a lot more like a civil war to me.
To answer your question directly, there are degrees of moral equivalence. Seldom in human affairs is one side utterly evil and the other totally good. So most of the time either accepting full moral equivalence or rejecting it completely is inappropriate.
The question is (usually) not one of whether moral equivalence exists, it is one of how much in a particular case.