Leliana does come off as somewhat creepy. I'm not sure if it is a writing disconnect, or if Gaider intentionally meant to do that, for that ambiguity.
A person who is truly repentant would have a different outlook towards her past actions. There would be true remorse. Lel, instead, rationalizes her past, and defends it. Like someone else said, she doesn't know how to tell the truth, even to herself. She wants to repent but she doesn't really know how to go about it. She has the vague feeling that her old life was bad, mainly because Marj betrayed her good, but if you really get down to it, she doesn't know *why* it's bad.
So, if your PC just superficially has a 'beautiful romance' with her, without ever confronting her about her paradox... then everything's peachy keen. Just sweep it all under the rug, love in blissful ignorance, and pretend it's all healthy. It might never turn up again; she's skilled enough to bury it way deep. But beware if it ever does come up -- she will have a mental breakdown. And you won't recognize your faithful lover. Because she was never truly what you told yourself she was.