That's my take on it also. There are hundreds of Unix programmers who will go over Microsoft's changes with a fine-tooth comb. It would be a disaster for MS if they find anything.
So I think MS is playing it safe and keeping it clean. They'd be crazy to risk adding anything questionable.
They will not put malicious code in the FreeBSD. But, does anything interpret, bootstrap, or manage FreeBSD? If so, that is where the malicious code will be.