If Bill Shatner writes another novel in his 24th Century Kirk series, there's a good chance he won't include Janeway's death.
What makes you say that? The Shatner books have, so far, tried to follow the 'mainstream' continuity of the novels, even if they do not reciprocate. Shatner himself may not be up to date with all the details, but the Reeves-Stevenses are quite good with continuity.
Janeway was killed, as far as I see it, because a story about her crew reacting to her death and moving on would be much more interesting than Lame Excuse #7 for her position in the Admiralty to somehow involve her taking command of Voyager for a while. Would you have been happier if the Voyager tie-in novels continued without her in any significant capacity (which they would've eventually had to do anyway) with her still being alive? This way, her character's death gets to make a real impact, instead of just slowly fading out of importance.
Lame Excuse #7? When did we get to Lame Excuse #1? Even if one accepts the unwieldy hypothesis that Janeway's character was going to becoming stale in the admiralty and this required the character being killed off, why not wait until then instead of jumping the gun like this?
As to the question - yes, I for one would have been happier with Janeway fading into the background than being fatally violated. That she would still be alive means that even if the character becomes second-tier, it can still be brought back to the fore at a latter date, which is harder to do when the character is dead since it involves resurrection and all the associated problems that come with it. And I don't think it would have been as damaging to the characters as others seem to think; Ben Sisko's been doing fine as a second-stringer and a de facto civilian.
Fictitiously yours, Trent Roman