BUT (and this is what is amazing and rare) both the narrative and the characters realize that that doesn't actually matter. Love is great, and important, but it doesn't conquer all. It can't fix Mitchell. And given that, the fact that they have this ~big epic romance~ doesn't make them more important than the people he might hurt.
THIS! This so much! Like you say, it's so painfully rare. I still think that this (from ep 7 when she's discovered what he did):

Mitchell: I love you.
Annie: Do you have any idea how inadequate that sounds?

might be my favourite lines from the whole show. THANK YOU SHOW! Now we just need to staple it to the forehead of every other writer in the world.

As Annie said, who the hell did Mitchell think he was in love with?
I love Mitchell because he's very fascinating. But I adore Annie for being flat-out awesome when push comes to shove. So often people talk about a character being 'the heart of the show', but Annie showed just how much determination and strength it takes to stay true to that.

This wasn't just a perfect end for Mitchell, but a perfect one for the ship. Annie will always remember and love him, and now she can remember and love him as a man who, eventually, did the right thing.
Indeed. And that too, is often far too rare.