2-ply: There may indeed some lingering agreements, though I would be surprised if he had signed exclusive development rights over to them for future works. That’d just be silly. I don’t know any writer who’d sign such a contract… 2001 was a different time. He’s made his feelings about Fox and their handling of stuff quite well known since then, in quite a few interviews with the press. (Do a quick google search for “Whedon never work for Fox again” and I bet lots will come up…)
Interesting article from LA Times about Dollhouse and the Friday Night Deathslot (which also makes mention of Joss swearing he’d never work for Fox again, back in the day:)
Another recent mention about the Dollhouse/Fox issues, and Joss’ past with Fox (and the fact he’d sworn never to work for/with them again):
Neither of those blogs lay the blame on Fox. The LA Times blog talks about the timeslot while mentioning Whedon’s rewriting of the scripts. While the other one mentions the article writer’s hunch that Whedon is covering for Fox with his announcements that it’s all his fault.
I still think Fox has changed, look at their treatment of Fringe. In any other year, it would have been canceled long ago, but here it is, still kicking.