The feeling I get through the series is that, for Janeway, the feelings may be there, but she doesn't think she can let herself have them AND be an efficient captain. Whether that's true or not from our perspective is irrelevant, Janeway seems to think this and continues to rebuff Chakotay. I don't think it's that unbelievable that he might give up trying after seven years.
But ending up with Seven? Yeah, that was a bit
Although, a pet theory I enjoy entertaining is that Admiral Janeway, who has obviously changed enough to think it's perfectly alright to try and go back to alter history, could also have changed enough that she may also see going back as an opportunity to rectify the fact that she pushed Chakotay away. After all, she knows herself, and she knows Seven. Who's to say she didn't drop the bombshell (that Chakotay and Seven get married) knowing that they would each react exactly the way they did:
Janeway, when told Seven dies in the arms of her husband, doesn't repeat "Seven" or "dies" but the word "husband" with a look of consternation. If you take into account that the crew seems unable to keep secrets and Janeway is Chakotay's friend, it's not impossible to think that she has at least an inkling that Chakotay and Seven are dating. Thus the repeated word and the dismayed look are a reaction to the fact that she just extrapolated the most likely husband for Seven. Especially if (and this works nicely into the theory that Admiral Janeway is attempting to do this on purpose, since she's also about to send them back to Earth waaaay earlier than she herself got back) there was a part of her that hoped Chakotay would remain available indefinitely so that once they did get home and went their separate ways (career-wise) then she could allow him to pursue her.
As for Seven, if I recall correctly, we don't get any kind of absolute affirmation that she and Chakotay stay together. In fact, it's pretty telling that her reaction is to immediately pull away, even knowing that they're working on changing the timeline and thus taking away the situation in which she dies. Given her issues with attempting to become more human and less borg, I can easily see this being a concept that continues to bother her and, as a result, she continues pulling away from Chakotay, even once they're back on Earth.
Like I said, though, it's just a little pet theory and honestly, it could be tweaked to suit the Janeway/Seven shippers, too.
All in good fun.