I definitely can't see any systematic favoritism, but I think the handling of the two non-white and non-male flagship characters of the franchise have been thoroughly mishandled in lit.
Again, you can't deduce a pattern from so few examples. If you want female or nonwhite characters to be treated equally, that means they're equally at risk of having bad things happen to them if it serves the story. It's contradictory to say you want equality and then cry prejudice every time a character who isn't a white male suffers a setback. Fiction is about
bad things happening to the protagonists. It's about people facing crises and challenges. So it's bizarre to assume that if a given character is faced with a crisis or a challenge, it's because the writers have some special animosity for them.
If anything, the common thread between Sisko and Janeway that might explain their handling in the literature is not their ethnicity or sex, but how they were positioned within canon the last time we saw them. Picard and Archer were both captains in their latest canonical appearances, as was Riker, so it's straightforward enough to continue them in that role. And Kirk was a captain for most of his chronicled life and we know how that life comes to an end, so there's really no new place you can take him (short of Shatnerverse resurrection, and that comes with its own controversy). But canon promoted Janeway to the admiralty and took Sisko to be with the Prophets. They were both canonically removed from command/starring roles, so the initial conditions faced by the novelists having to move their respective series forward were different from those faced by writers dealing with Kirk, Picard, Archer, or Riker. So that alone is enough to explain why those two characters were handled differently than the others.
In particular, I don't understand the objections to taking Sisko to a place that's uncomfortable for the readers to see him in. I mean, where was he in "Emissary?" He was a depressed, broken man at a low point in his life. That was the initial problem that his experiences in the series helped him to deal with. What I see in Rough Beasts of Empire
is the beginning of a new arc for Sisko, one that starts with him in a similar place to where he was when we first met him. It stands to reason that his situation will evolve as the books progress, just as it did before. DS9 has always been about characters going through big changes, often suffering painful setbacks and losses, and having to find their way forward again. For a lot of its characters, DS9 was about journeys of redemption or healing or self-discovery. If a character starts out happy and fulfilled and content, where would you go from there?
As for Janeway, I don't really know why the decision was made to kill her off, but I think Full Circle
proved that killing a character doesn't mean mishandling her. Kirsten has handled Janeway's death and its impact on her friends and loved ones in a magnificent way that's made it very meaningful. If she were still alive as an admiral, giving the ship its assignments from a desk somewhere or constantly being given contrived excuses to join the crew on mission after mission, that wouldn't be a very meaningful role, just a contrived way to keep the character in play after she'd been canonically placed in a peripheral role. But having the characters have to deal on an ongoing basis with the emotional consequences of her loss makes her absence important and powerful, and makes her a more crucial character even though she isn't physically present.