Yeah, Palp knew that some jedi were out there. Not all Jedi had Clones on them, just the more experienced such as Obi-wan, Mace, Yoda guys like that. So thats why after Anakin becomes Darth and is put in the suit, they have a
crack down/mop up operation for the remaining jedi out there, the very very very few. But there are a few things in EU when old jedi from the Republic way back when come out of hiding and join the new order.