I never liked the whole C/7 thing; it just appeared out of the blue with very little background in my opinion, plus the idea of Seven getting together with Chakotay after having a romance with a holographic version of him is just plain creepy.
It was already said in the thread that Seven has the cortical implant that bascially shuts down her vital systems if she experiences hightened emotions, so you have to wonder how that all worked (of course I guess it could be just as easily supposed that the Doctor removed the implant at some point...).
If the writers had wanted C/7 to work they should have shown some sort of degredation in the relationship between Janeway and Chakotay (because even in Endgame there was still more freaking chemistry between the two of them than Chakotay and Seven!) and then shown how Chakotay and Seven's relationship developed as a result.
I will always be a J/C shipper, and though it never happened on the show I say that something could have happened in season 7 (before all the C/7 nonsense) after "Unimatrix Zero" (I mean, come on, them holding hands on the bridge! How does that not scream romantic subtext?).
And when they returned home, absolutely they could have had a romantic relationship. As for Janeway being 'fate's bitch' I'm going to quote the good Captain here and say 'the hell with it.' Let Janeway have a little happiness.