You posted 4 subjects here, but I'm just going to sum it all up here:
Nothing you have said was remotely correct about the movie. I think you wanted this movie to be so much about how horrible a convent is that in the end that's all you can see. I think you missed out on a great character study by not seeing the subject matter under a different light than you're own bias.
The Nun's Story isn't about how horrible a convent is. As a matter of fact I think it does a GREAT job at showing that it's not as bad as people think it is. All they're doing is seeking self actualization through meditation and routine. Every religion has that. It's not a bad thing just because it seems boring or hard to do. And what does the movie show? Nuns caring for people all over the world, studying advanced sciences, learning to put others before themselves. What's wrong with all that?
Sister Luke doesn't hate the convent in the end. She just knows that in her heart she can't be a proper nun, even though everyone else thinks she's great, But she went into the convent for the wrong reasons and she's accepting that. But she still respects the convent and crosses herself at the end. Just because she's leaving doesn't mean she lost faith.
And everything else you said. Yeah, you lost the point completely.