I think it is quite likely that Janeway reciprocated Chakotay affection, but that she was also dedicated to her position and responsibility to the point of sacrificing that to duty. Viewers tend to think of Voyager as "TNG Lite" and forget the true danger they faced and the isolation they endured. They literally had no backup whatsoever, and the responsibility that Janeway faced had to be terrible.
As for the Admiral, well, her motives are not very well defined. It is out of character for Janeway to throw away two decades of history simply because she wanted to get home sooner, yet that is all we are shown on the finale. It is only natural to speculate about other motives, personal and professional, in order to make her actions more forgivable. I like to think there were many issues that made her do what she did, including having a second chance at a relationship with Chakotay. There is some very fine fanfic that explores this situation in hundreds of different ways.