What if the cyborgs work for another branch of W&H? The Senior Partners might be unhappy with the way Angel is running things, so they send some operatives from the another branch to take control of him. Maybe they have always had a mole in the Watchers council, and that's how they got the informatin on Wesley's father.
That's how they could have found Angel in the first place, from Giles' reports. They wouldn't be interested in the Slayer per se, because Slayers are so replaceable, but the mole would have been planted just to hear about vamps with souls. I realize that Gunn's line about them killing demon's doesn't support this theory, but it would be interesting.
Or, as someone else suggested, it could be renegade Watchers, after all, that's not an unprecedented occurance.
I briefly thought of the Initiative, but I don't see how they would have gotten the info on Papa Wyndam-Price.
I guess we'll all just have to wait until Joss let's us in on the secret.