Even though she says she's been murdered it's really just a reboot and update.
As for the marbleization it's reversible. In season 4 Bad Janet marbleized our good Janet. Later after being transported to The Bad Place, Bad Janet un-marbleized Janet.
Janet isn't "alive" (She is an anthropomorphized vessel of knowledge) so I don't think she can die in the real sense, even when she is murdered and updates. She can be marble-ized but that's not really the same thing since it's reversible. It's more like a low power mode for her.
The Doctor once said he goes to a void when he is deactivated. My head canon is that he goes to the same void as Janet from The Good Place and they hang out. Or maybe it's Derek's void he ends up in.
I'd be ok with Gary killing off my character.
I wouldn't be ok with dying to that idiot Armus.