They've taken jabs at the Bush administration before. The reason they are pro-military is because they rely on the Air Force for support. They made the NID as a way to tell anti-military stories without actually involving the military. Sokar was the Christian Devil, and the entire Ori arc were pretty much a take on the Jewish-Christian-Islamic religion.
Light jabs at George W. Bush hardly count as political engagement. You'll have to enlighten me on where these jabs actually occur also, besides Jack's "shrub" comment about Kinsey. The fact that, after viewing the entire series more than twice, I can't remember these jabs isn't indicative of them having much potency, but my memory could just be a fault.
The NID is a civilian agency, which undercuts any "anti-military" sentiment of the stories. I totally understand why the series is so pro-military-- the closest its come to being anti-military is a bad commander or two--characters who are always repentant of their poor leadership (or in the very least punished for it) in order to glorify the military heroes of the series. But let's be honest and admit to ourselves that Stargate's pro-military sentiments are prevalent.
Sokar was an Egyptian God. "Satan" was only mentioned as one of the guises he took on, and, besides, the character didn't even last an entire season.
Lastly, the Ori arc goes out of its way to avoid talking about Christianity, Islam, or Judaism. The show can't even mention Jesus Christ when talking about immaculate conception, preferring a Darth Vader joke instead.
None of these comments are to take the series too far to task. I love it for what it is, at least as far as the eighth season. After that, I've found it wildly inconsistent, but that has nothing to do with its politics.