Some interesting points you raise, I'm not sure if lack of intelligence or knowledge should be seen any differently as someone knowingly doing something bad. Maybe it makes things understandable but it doesn't take away from what happened. Though I also feel if you have know knowledge of something being bad then it is unfair to punish them the same.
I think that comes down to being dependent on situation and I think in the example of Mother Teresa she full well knew the consequences of people not using contraceptives and how that can spread disease, so she should be held accountable.
I also find it difficult to say whether 'the means justifies the end' as again in some situations it will some it won't. It really is a difficult question of morality, good and bad are different from person to person. Also causing harm is something that can not be avoided someone will always be harmed to some extend in making change.
I don't like to think of people as good or bad because there is just too many arguments for and against, I prefer to look at it as people are people with individual motives, good or bad matters as much as we each make it.