I think they'll stay together because BoB knows that Watson is his only ticket to NFL success and McNair/Smith don't want to stunt his growth by forcing him to learn a new offense.
We'll see if FO can find an HC suitable for Watson's style of play. If not, a contract extension would reduce any tensions.
I mean, I'm not usually one to defend BOB, but Watson did have over 400 yards just this week....It's not like BOB is holding him back. Sure he went conservative at the end, but if the O line did their jobs (including if the "best O lineman in Texans history" doesn't get blown up and allow a TFL killing the drive) then the Texans win that game. It's kind of hard to see how far Watson has come this season and think that there's anything wrong with the way he's been coached.