I don't think people really feel that the novels will be better served without Janeway do they? The polls that have been conducted here show that people like Janeway for the most part.
I think the confusion here is that people seem to be conflating "characters I like" with "stories I like". I don't really give a crap about what happens to characters in an absolute sense, as long as the stories are good, and if the best story happens because of killing off my mostest favoritest character, then I'm pretty much ok with that. I can give you a few TV shows and books that have completely blown my mind with similar plot twists. Jericho and Angel come to mind.
The only possible exception I can think of to this rule would be if Calhoun died in New Frontier, but that's mostly because now that Shelby has moved on, Burgoyne would become captain, and I really don't like Burgoyne at all; I feel as though a story about Burgoyne as captain would be a bad one, I'm not interested in watching that character develop in that way. I'd still read it if it happened though, and give it a chance to surprise me; I love PAD enough that there's a solid chance I'd still like it, I think. But aside from that, as long as they felt it was worth it, I'd be all for just about any character in TrekLit biting it. Picard, Troi, Janeway, Reyes, Spock, Trip, or whoever else. As long as the story was worth it.
And also, on the flip side of that, just because my favorite characters are in a book, it doesn't mean I'll like it; the amount of useless crap in the trek line that has happened to star Picard or Data, for example, is fairly staggering. Characters are only as good as the story they're in, and I'd rather the story be the best it can be.