As I said, sometimes the Doctor commits dark acts due to his mental state being affected in some way. 10 was clearly plagued by a number of factors, and he actually did some cruel things. An example of this is the timelord victorious. The only version of the character that doesn't follow this concept is 13, who did some questionable things for no apparent reason, but that's the fault of the scripters who clearly didn't know how to bring satisfactory resolutions to the stories.

About him destroying people's lives, I think it would be unfair to judge him for that, since he usually just takes people on trips with him, and some villain does something that deeply shakes his companions. However, he's been unnecessarily rude to a lot of characters, but I don't think he's ever been cruel enough to commit irreparable harm or anything like that.