AFAIAC, if Carey is not writing a TOS book she's totally slagging on the characters.
I thought her novelization of Voyager
: "Flashback" was great. She had to double the length of the story, so she added a really good Kes subplot and a Paris subplot, and she expanded on the ending in a way that made it much more about Janeway's character rather than the pure technobabble climax of the episode. So I'd say it treated the characters pretty well.
Carey's VGR Captain's Table
novel Fire Ship
is also pretty well-regarded, I think, though it was almost exclusively about Janeway.
Her Dominion War
duology adapting DS9's opening season-6 arc took some liberties with the story, but she added a plot thread that made Sisko a more active guiding force. I don't think that was treating him negatively.