Besides, if the killed him off can you imagine the complaining that would still be going on? It'd be worse than Trip.
Bah, what do you want, I always thought that, for an actor, a fond and/or an emotional farewell (or even a shocking exit) for her/his character was much better than to stay at any cost and get lost in certain "anonymity", to the point that viewers do not notice even anymore her/his presence on screeens. It's frustrating for the actor AND for the viewers who feel that something is not right, what annoys them more.
As for a possible loss of a popular character like Chakotay, I know that it would have shaken a double fandoms (RB's and Chakotay's) but it would have followed a certain logic
(and when we perceive the logic behind such a decision, it often easier to apprehend the possiblilty, even if we still don't like the scenario!)
1) For Robert Beltran, a desire to leave an adventure where he has stopped for a long time blooming and where he felt wasting his time. I think that, at a moment, if an actor like him has a minimum of self-esteem, instead of waiting (and even trying) to be fired, he would have taken himself the decision to leave when the occasion is offered -> smoothly or with losses and crash! Seen the sad “show” which RB/GW offered, they certainly tried to be fired to get interesting financial compensations and to victimize still more. But in the end, both committed professional suicide, even if RB seems to get easier!
2) For the producers, to find a way to get rid of a cumbersome and whiny actor, in using a clever storyline to justify his departure. IF they had acted as jerk as they did with Jennifer Lien (with Fury, which they accepted the scenario which ruined the so charming and sympathetic character who was Kes), they could have presented Chakotay at his best and killing him off at the end of a double episodes -> fandoms (RB, Chakotay, J/C) would have had what they wanted/waited for so long: an episode entirely focused on this character and a J/C love scene. And if complaining had continued, producers could have answered that, it was an artistic choice although, knowing that killing-off one of the most popular characters of the show would be painful and unpopular for his fans.
3) For the storyline: at least, in Endgame, Capitain Janeway would certainly had a better understanding of the actions led by her older doppelhänger, Admiral Janeway. Indeed, both having already suffered of the loss of someone who was very dear to them, Chakotay, in DQ (and the Admiral not yet over, almost 30 years after) and the announcement that Seven was going to die as many of the other members of the crew and that Tuvok was going to become crazy, for lack of having received the good treatment in time, would have allowed viewers to better apprehend Admiral Janeway’s actions,
even if it’s still not morally totally right.
Hey, they even killed Kathryn Janeway and you know how much I like the character her performer. But, if it was a personal choice from the actress (besides, it's her idea to kill-off one of 2 Janeways!) or a logic end for the character, it would have been alright for me!. So, why not the same for RB/Chakotay?!