I think she's right!
Honestly, there have been too many "pairing offs" in too many series (not only Star Trek) between characters who haven't had any chemistry at all, just for the sake of it.
I think that Janeway was right in her statement and I also think that the writers did handle it good. Until the last episode!
However, I wouldn't have objected if they had came up with a "happy ending" between Janeway and Chakotay in the last episode. That's what many fans wanted, there was a chemistry between Janeway and Chakotay and it would have been perfectly OK when the series was about to end.