No, he's not done. The profit margin on those movies is just fine when ancillary and foreign are added in. They don't toss $100 mil budgets at someone just because he has a development deal with them. George Clooney's made nothing but huge losers and he's far from "done"--Cruise movies consistently make over $100 mil; Hollywood looks for someone who can open a movie, and Cruise does that. The profit margin is more about the studio and the producers.
Crusie hasn't been kicked out of the industry; he's just lost a development deal. He no doubt has development deal offers from every other studio sitting on his desk right now. This kind of thing happens all the time.
Unless he signs onto a helluva blockbuster script, I still say the public is sick of him and his strange antics. Don't think he'll bring in the masses anymore. Say what you want, but he's a freak and makes people uncomfortable and not willing to shell out good money to watch him on the big screen.
The only problem with this is the studio's statement. If this were just a run-of-the-mill business deal, they should have issued a boilerplate statement about how Paramount and Cruise "mutually agreed to pursue other ventures" or some other such feel-good mush. Instead, Sumner Redstone called out Cruise's behavior.
There's something else going on here - my feeling is that Paramount has just fired a shot across the bows of all the A-list script readers in Hollywood. Namely, I think they're saying, "In case you haven't noticed, our industry isn't doing so good these days. It's time you guys shared some of the pain." It'll be interesting to see how the rest of Hollywood reacts to this, as well as the Scientologists.