>>723913503
I think his dialogue with captured Gordon, Alyx and Eli in his office shows this extent the best, I can't recall the exact wording without looking it up again but a lot of what he says sounds like he does keep a lot of cards in his own hand to play, at one point exclaiming that he now has all the pieces he wants to make all sorts of bargains with the Combine.
So to me it would seem like he does have quite a bit of autonomy. If nothing else because the Combine can't be bothered to concern themselves with all the trivial concerns of humans and that's exactly what he's for.
Whether or not the Combine would be still on to anything major he's scheming on his own would be a different matter.