There's book smart and then there are street smarts.
Conan (and/or his agents and lawyers) didn't read the contract too well, which is why he is getting fucked with. Jay Leno made sure his contract was as tight as possible, which is why he is staying. Conan might have graduated with honors at Harvard but he's pretty much at the mercy of NBC, which isn't very bright at all, considering they can threaten him by moving his show past Carson Daly's. Not only that but he doesn't have much of a backup plan. He might score a few gigs after his cancellation but that is pretty much it for him. Maybe he'll be a once in a year writer for Rolling Stone? Maybe The Huffington Post? Maybe some bit sitcom that falls through? A guest host of The Daily Show? He has little future ahead of him.
Jay Leno is conniving and probably not book smart but he's managed to usurp two successors, have nearly a billion dollars in the bank, and had a contract that made sure he would never go away quietly unless he chose to do so.
I really fail to see how smart Conan is in this whole thing. He got railroaded without much of a backup plan. He got outsmarted by someone who went to school for speech therapy.