I would've definately had a problem if they established their relationship while she was still being imprisoned by him, which would've definately spelled "Stockholm" to me instead of any real genuine feeling.
However, there are several good points that keep this film from being an absolute mess to me:
-He lets her go.
-She immediately runs out of there. If she were a "Stockholm" victim, I'd see her as being compelled to stay rather than going with her first instincts.
-Her renewed happiness. It's natural that she would be relieved, but she seems "cured" of all her trauma and I was wondering why this was so...
-Thinking about it now, I think seeing someone else who is suffering and doesn't know how to deal with their lives in a healthy way makes her feel that she is not alone (it also helps that he freed her from imprisonment).
-I could sympathise with her curiousity: I can see myself going back to check on him as well, confident that he won't try to lock me up again.
Going back to the old adage, if you love someone, set them free..." Maryanne, being on the outside again, had a chance to refamiliarize with her surroundings appreciate them and her life.
Even if his techniques were odd, unhealthy, and frightening, Maryanne seemed grateful to Mike for snapping her out of her stupour. Also, I think Mike can be forgiven since he seemed just as messed up as Maryanne was and needed time to figure out what was ultimately the right thing to do.