I'm sorry to say this, because I did like the character, but given their decision not to do anything significant with the character... they should have killed him off. In a properly heroic manner, of course.
One, it would have been an emotional gut punch for the audience, and a reminder that the Delta Quadrant was dangerous, and no one was totally safe.
Two, it would have Janeway a stronger first officer in Tuvok. Maybe he could have reined her in a bit more when she went a bit nuts.
Three, while I agree that it was probably right that the J/C ship didn't sail, I think there were some unresolved feelings. A deceased Chakotay might have let Janeway confront those feelings without being in a position to act on them.
4. If they did it early enough, they could have kept Kes (and Harry) and still gotten Seven.
We'll see what happens with him in "Prodigy"... hopefully, it will be good enough to make me eat my words.