Coincidentally, Paramount have just signed a deal with Trey Parker and Matt Stone.

I think this parting of the ways is down to a number of things:

1) Big salary, star-driven movies are one the way out...concept is now king again.
2)Cruise ain't getting any younger
3)Scientology bullshit, like threatening not to promote MI:3 because of that South Park episode.
4)MI:3 bombed partly due to negative publicity surrounding Cruise's reaction to the South Park episode, his wacky plans for the birth of his child, and his outburst on antidepressants.

He was becoming a bigger liability by the day, and I think they've done a smart thing in cutting him off.