I have a nerdy, extremely involved PC in this campaign and I'm trying to figure out a way to pull him out and retire him rather than having the DM kill him off. Any ideas?
The campaign makes us pawns of deities and he's a thoroughly invested Pathfinder.
How about a crippling that magic can't heal? Not enough to actually take him out, just enough for a limp that makes him retire and go into training others?
Do they have any family/loved ones?
You say nerdy and stubborn, so my first thought is some mystery that presents itself that this character alone must solve. A mystery that requires extensive research. The character's nerdiness should make such a task appealing and the stubbornness a source of determination to see it through.
I'm talking extensive research. So much research that the character will probably have to devote a long period of time, or maybe the rest of his/her life. Research that prevents adventuring. It will require careful translation of countless books in a lost tongue that require one's full attention to thoroughly comprehend. The kind of task that requires one to find the missing links between multiple different sources to arrive at the sole conclusion.
Of course, this is the assumption that nerdy is equating to booksmarts/scientist-like. If that's not the case I'm sorry for taking your time.
Do you like role-playing this character?
If so, then instead of coming up with reasons that the character should not continue with the party you should come up with reasons that the character should continue with them.
Have them find a library of ancient lost secrets. Have the caretaker die and make the charcter the new guardian. Now he spends the rest of his life protecting the library and you can get a plot hook out of what he finda and he can act as a mouthpeice for important info from the GM.