I don't see that it's a particularly thoughtful or subtle mirror. It's all, "hey, the Genii are like the Taliban the way they hate us, let's have them do something awful and then we can have a morally-complex discussion about the appropriate response!"
It's a reflection of a certain type of American foreign policy, but not a reflection that really informs us particularly well. But then, neither did the Star Trek analogies.
Oh yes. I didn't mean to imply that it was a thoughtful or subtle mirror. But I think mirrors the simplistic & polarising Us/Them approach to otherness which Bush & co like to evoke with their "axis of evil"/ "war on terror" soundbites, in a way that, say
Firefly
or
Farscape
does not. I think it's fair to say that SG promotes a (shallow as hell, but then what percentage of viewers are remotely interested in American foreign policy and/or own a passport? And what percentage cheerfully accepts stereotypes of 'All Muslims are X', or 'All Europeans are X', or 'All Communists are X' etc? And what percentage bought Freedom Fries, or thought that Osama Bin Laden was directly connected with Iraq? Most viewers AREN'T particularly subtle or thoughtful or sophisticated) robust image of American Human interactions with non-Americans Aliens (some of whom are okay, some of whom are evil) in which America the Humans retain the moral highground, and our value system is better than the other guy's value system, and one doesn't need to REALLY worry about things like the Geneva Convention, because after all, we ARE the good guys.
I'm not trying to have a dig at educated or thoughtful Americans here, incidentally - but I pretty much assume (and this is where my Inner Severus Snape is showing) that most people are kind of dumb, and that most people aren't interested in foreign policy unless/until it has a negative impact upon their day-to-day life. I think George Bush's pre-Election schtick about how simple it was back in the days of the KlingonsCold War (when everyone knew who the Them was, and how it was all a bit more complex now, but that there was still a Them out there)...well, I think that struck a chord with a lot of people. And now, with terrorism becoming more of a reality for the US, the whole business of Go'aould hidden enemies, friends who can become enemies is a different paradigm.
I certainly don't think that SG is deep or thoughtful, or that it's consciously making much/any effort to reflect America's foreign policy - but I do think that these concerns bleed through into genre fiction and television.