I don't think you get it. It's not about Kate Mulgrew. It's about Kathryn Janeway as the captain of Voyager.
It's about watching a show and starting to like it because of the characters and the chemistry between them. It's about wanting to read about the same characters when the series is over. Not to see a favorite character or the
favorite character being killed off and replaced by a character who simply can't replace the old favorite.
It's about emotions, it's about liking certain characters in a certain series.
And I must say that I do find it a bit insulting to suggest that the Janeway fans should abandon Voyager and concentrate on Mulgrew's current career. I wouldn't have been particularily happy if someone had told be to watch "American History X" every day when Kes was dumped fom Voyager (not that I don't like that movie, it's great).
As for your comment about Neelix, what I know he's only making a "guest appearance" in the book. Not to mention that Janeway, Kes and Tuvok are still missing.
No, I haven't read any TrekLit book with female captains other than those who show up occasionally in a story. So far I haven't seen anyone who I would like to see in charge of Voyager instead of Janeway.