You have the right instinct, narrative takes a backseat to player comfort. Don't worry if it makes sense in-game, that's not a real concern. Do whatever tying up of narrative threads you want, after you're sure the player is comfortable out-of-game.
If the player wants, just let them start the next game with a new sheet. If they want to do a sendoff, do it at the top of the session. If they don't want to acknowledge the old character, then they just evaporate and a new one is inserted.
Ultimately you're playing with friends, and the reason everyone is there is to have fun. The group's fun should take precedent over everything else.