Paramount doesn't own Cruise. His dealings with them are on a picture by picture basis. It is folly to suggest that they are intentionally sabotauging their summer blockbuster to gain the upper hand with him in future dealings. If this flic fails these folks will be out of a job. If it succeeds wildly then they will gladly pay Cruise whatever he wants next time.
I don't think it will "fail". But I do think they have manipulated expectations. Look at the headlines: "$48M opening is a failure". Doesn't that strike you as odd?
Cruise has a sweet-heart deal in Hollywood and he does need to re-negotiate this. The Wall Street Journal has covered this.
The studio wants to make money, and it wants to have more power than the actors. The publicity for MI:3, as I see it, will allow the movie to be profitable, but decrease Cruise's power. That's a win-win (but not for Tom).