But I agree that was the wrong decision. That does not make God or Christianity evil. That makes what they did evil and the God they created evil.
What is the difference? The deity you claimed they created as opposed to an objective, genuine supernatural entity. For me this sounds even more like a cop-out, that God is always good but his followers bad, God gave people freewill but only to Christians and that there really is no true Scotsmen.
Yes, you said that the decision those wicked missionaries or Padres made were wrong but so what - the end justifies the means? There is no giving Indians their faith or culture back, no way of recreating the codices and no way to unbreak hearts.
Correct me if I'm wrong but wasn't your justification that those evil people did what they did because they wanted to save the souls of the savages. They thought that was necessary, noone else did. Evil in my book.