Well anything is possible but the most likely explanation of things is usually the simplest. So I think the ISIS elements had him all along.
Assad may be a dictator, but his dictatorship did not try to commit mass murder on different religious elements within Syria. The alternative dictatorship/caliphate that ISIS would set up in Syria on the other hand would add a newly expanded dimension to the definition of MONSTROSITY.
Except for one fact in the story that tells against it. And that is that there were apparently some kind of negotiations going on with Syrian diplomats regarding Foley's release. Now, maybe Assad's people were just playing along. But if they didn't have him, don't you think that at some point they would have just come clean and said “sorry, it wasn't us”?
I guess I'm more inclined now to think that Foley was being used as a “bargaining chip.” It's just that he got bargained away to the really bad guys.