Studio might not let Cruise perform his stunts now.
Why? The insurance covered the extra expenses. Unless another insurance payment on Tom Cruise would cost them way way way more, I don't see how that would make them forbid Cruise doing his own stunts, which are the highlight and selling point of this franchise at this point. People go to these movies to see what crazy stunt is Tom going to do next.
If the movie doesn't have legs and fails at the b/o, they might reconsider ever doing another M:I movie, but if they make one, I'm sure Cruise is doing all his major stunts once again.