If the surface of the planet was poisoned, how did the "enemy," the Breeders take over most of the planet and survive up there?? The visuals show the Breeders bombing buildings on the surface. What would be the point of that if Alar's people were deep underground?
Why didn't SG1 try to establish contact with the Breeders faking an attempt at diplomacy?
Why would the stargate be located in a tunnel instead of outside?
Then there is another issue: O'Neill decided to doom Alar and all the stasised people to destruction because of their racist ideas, without any hope that they could even change their minds, and without a diplomatic option. I think this is also a bit problematic. Why didn't the new "allies" from Earth seek to enforce a surrender instead??