Could be. With all the alternative theories floating about, one is that Manafort was a Clinton/Obama (FBI/CIA?) mole all along. I sort of doubt this at the moment, based on his indictment, but if he gets completely off the hook later for what does appear to be serious financial fraud, you’d have to wonder.
I wouldn’t rule out anything, but being a CIA op is way down on my list. They either didn’t have anything on him before or they decided to hold off on charging him until a golden opportunity like showing up in the Trump campaign.