Oh, I agree completely -- the problem is what the show tells us (tacitly) is a Proper Happy Ending, based on how the Musketeers (and their respective endgame ladies) finish out the show. (Which is just one more part of a long rant about the show's handling of female characters throughout all of the seasons that I probably shouldn't get into here.)
And you're right, we weren't told much; what we were told, and what we're given, to me reads as if they're telling us that "LOL no she's evil and she was always evil and she went right back to being evil so clearly she was unworthy". Someone on Tumblr described it as a vicious loop of "does she kill because she's unhappy or is she unhappy because she kills", and while S2 pointed to the latter with her desire to change, I find the handwavy reversal in S3 forced at best (and a total waste of a character and kind of illogical besides, but that's another soapbox).
That is the problem I have in a nutshell, especially when his actions towards her are (and always have been) without consequence.
... wait, I said I wasn't going to go climbing on soapboxes, didn't I?
Anyway. I'm in the minority on here in that I have a lot of can't regarding S3; I like some of the high-level ideas but I find the execution to fall flat both broadly and specifically (with a few exceptions) and to include some very serious problems. I'm glad people liked it, and I'm glad there can be civil discussion about its merits and flaws, but I'm definitely not in that happy group. (I'll just stay in my own little world where there are only two seasons instead. XD )