So now you're conflating the misbeliefs of people with what the religion actually says.

What you call the "misbeliefs of people" are what the religion actually says, or at any rate what they think the religion actually says, and would not hold such beliefs in the religion's absence.

people who were against those things were not doing so based on the pure beliefs of christianity.

They were doing so out of the belief that God wanted them to, regardless of whether or not the idea was rooted in Scripture. Again, they would not be doing so if not for their religion. Also, the second commandment is pretty clearly against any idea of freedom of religion.