There is little doubt in my mind that they offered Manafort a deal. And he refused, and took his chances. And yes, it was likely a bad move, in that he will likely die in prison. However, that is better than dying from polonium poisoning, and his family also being murdered. Manafort essentially stole millions of dollars from a Russian Oligarch with direct and close personal ties to Putin, and he has been hunting him down. Manafort flipping would have likely ended with a much worse fate than rolling the dice with a couple of trials.
Hopefully he is, I agree. But I have serious doubts about it as well. Gates is the scum of the Earth, just like Manafort.