York is a useless contrived walking plot hole, not a character.
If Oda wants to give Vegapunk (Stella) an arc, by the end of Egghead he'll realize that desires and logic both are what make a round human being, so him having split his more basic needs into another being was a mistake (hence the betrayal). Him forgiving and "reabsorbing" York would be the way to go.
I'd like to analyze Vegapunk's existence and title as world's smartest person deeper, but I don't have the time.
I'll limit myself by saying that I expect his research to help all the factions currently involved in the story.
He has empowered the WG with the various Pacifistas/Seraphim and who knows what more weapons.
He's told the SHs a couple of things about DFs (and hope he'll delve more into the scientific aspect of it, not just the fantastical "People wish them into being").
He will be taken to the Revs, in one form or another (either as a full body, a simple talking head, or simply his digital persona in the guise of the Internet of Punks).
And, to fully show how science is neutral, neither good nor evil, but it's the user who wields it in one way rather than another, I expect whatever knowledge he's sharing with the SHs to also be stolen by BB, who will find a way of weaponize it. Thus you will have all four agents - WG, Revs, SHs, BB pirates - all using one man's research to
- control the world
- try to liberate the world
- bring freedom to everyone
- bring darkness to everyone
Only thus, in my eyes, the title as brightest mind can by justified: by providing everyone with the means to realize their own distinctive and at times opposing goals.