Ok - you all missed.
Gordan HAS BEEN working for the G-man. As in prior to HL2.
He's dropped in from out-of-time, suspended-animation, sleep, what-have-you, and inserted into the space-time continuum at the beginning of HL2 (you heard the other train passenger's comment "where'd you come from? I didn't see you get on") to do this job. Exactly the job he does - wipe out the combine.
I personally thought the ending was kick ass for one reason: they had the balls to wipe out your love interest. When you destroy the REACTOR at the end it sets off, well, what you're looking at is the expanding genesis of the deathball that is a nuclear explosion. Slowed waaaay down. At the split instant of the fusion reaction's explosive blossoming beginning, the G-Man again manipulates space/time to come and pluck you out of harm's way - for future use of course. After all you finished your job there, and you're so handy to have around.
That Valve scripted it in such a way that he takes you and leaves Alex, her dad, the lady scientist, and all the other thousands (millions?) of poor people down below in the city to thier soon-to-be-vaporized fate was ballsy IMO.
(Loved the "flicks dust off her lapel" move of his. Its a sortof "You're going to burn, but try not to die a mess, missy" gesture. Great stuff.)