Everton would be stupid to keep him this summer. His performances last season were rank, they won't improve this season if he's forced to stay whilst City march on with Pep.
In terms of it going to deadline day, I suspect John himself will take matters into his own hands before that. You can maybe keep a player one year against his will, but two years with a player of his quality with no European football, uncertainty over your other best players, and no real force shown in the market in terms of improving your own squad to stop it regressing never mind standing still ... yeah Stones will get his move. And if he doesn't then you will have a player who's value is going to plummet next season. As I say keeping him this summer will be pure stupidity on the part of your owners. But they're new to owning and running a club so they will make mistakes early doors.