It basically boils down to a question of cinematic versus realistic, and what your GM wants to run.
GURPS is a realistic system that has quite a few different "patches" that can be used to make it cinematic. Ultimately, it's got a second by second combat system, a horde of different skills, and a dice mechanic that's actually based on a bell curve. For a Stargate campaign, there's a GURPS supplement covering just about every culture that he'd be interested in taking you to.
D20 Modern is a "marginally" realistic patch onto a cinematic game engine. Neither combat nor skills are as detailed as they are in GURPS. However, D20M flows much faster because of that. You flat out will not find all of the different historical and alternative settings for d20 as already exist for GURPS. However, if you already *have* the GURPS materials, the background material is essentially rules-free, and most settings aren't going require all that many special rules.
So, IMO, it boils down to what he wants to run. I'd confess I'm all that familiar with the SG-1 TV series. But, even given that fact, different GMs have different approaches. If your GM is running a campaign for a group of highly trained scientists who are going to go into great detail on their interactions, or is running a game for a crack military squad that's going to go into hyper-detailed combat, run GURPS. If your GM is running a "high-adventure" beer and pretzels kind of game, run d20M.