Harry and Cleary
I don’t have a problem with their union in the end. Thing is, on rewatch and knowing what we know about the truth, I suspect Harry had put 2 and 2 together and figured out that he turned her in and why. That's what I think she implying when at the freak show, she accuses him of running a game on her. She may even be using her adherence to her vows as punishment towards him by the last two episodes. When she says "she can't" accept his proposal and he wants to know why, she turns and runs. I think she can't say it because to fully voice his betrayal would perhaps make it impossible to accept his love and return it. He called it in episode 9: she really did need to forgive him. She seemed to sleep on it (in 10) and decided to do just that because then we see in her face that she does love him. Cleary must have been right. She truly was happier with him than she'd ever been as a nun. Harry was always sharper than him in a lot of ways; I think she figured it out. So yeah, I don't feel bad about her being with him in the end. At least she had someone on her side when she was caught - which was going to happen sooner or later. Being a nun and an abortionist seemed like a pretty big internal conflict to be carrying around. Interesting that she never repented her actions, even to her beloved Mother Superior. She had strayed pretty far from the laws of both man and her religion and maybe that made it possible to accept the loss of her Sisterhood because of an amoral man's love.