I agree that it is possible to infer an anti-Iraq war slant here, but it easily possible to see it differently with other historical analogies.
For anyone who has seen a WWII movie, you could say that the Cylons are the Nazis and the humans are the Resistance. The humans are not attacking civilian non-combattants, and our troops are not rounding up truckloads of civilians to execute them.
Exaclty...
The leader of the humans is willing to store arms in a temple that the occupiers have respected as a place of religion. He is also willing to wage war near the sick and the injured and willing to send men off to commit suicide in battle.