He'd be ****ed especially from a Legends perspective. The Jedi would seize all of Palpatine's holdings and once they also arrest the Separatist leaders they'd have more than enough evidence to convict him of high treason and conspiracy. They had Gunray's Mechno-chair, they knew Dooku had visited the Works. Once Nute Gunray realized his cover was gone with Lord Sidious captured, he'd probably even sue for peace. Either way, Palpatine colluded with rebel elements of the Trade Federation to undermine the legitimate diplomatic efforts of the previous Chancellor during the Naboo crisis. There are communication records showing him conspiring with Gunray and Dooku. Dooku himself told Kenobi the Republic was under the control of the Sith Lord.
I don't even think the separatists even knew who sidious really was....
I think only Dooku, maul, etc knew but other then that no...he didn't meat the other sepratist leaders in person. In the novels I've read he only spoke to them via holonet
Also....how would they keep him in jail or anything when he effectively controls the army...DERP. They clone troopers obey him without question, the moment he wants he'd just tell them to kill everyone.