However, they sure did slam the EPA.
PA Soldier: I’m afraid we lost them, sir.
Russ Cargill: Damn it! Well, then you find ‘em, and you get ‘em back in the dome! And to make sure nobody else gets out, I want roving death squads around the perimeter 24-7! I want 10,000 tough guys, and I want 10,000 soft guys to make the tough guys look tougher! And here’s how I want them arranged: tough, soft, tough, tough, soft, tough, soft, soft, tough, tough, soft, soft, tough, soft, tough, soft!
EPA Soldier: Sir, I’m afraid you’ve gone mad with power.
Russ Cargill: Of course I have! Have you ever tried going mad without power? It’s boring, no one listens to you!
I like all slams on power, and The Simpsons has a tradition of attacking mindless bureaucracy of all kinds. But pay closer attention. It’s not the EPA they’re mocking. It’s the EPA as run by a Bush-y sort of ex-industrialist CEO guy. I don’t remember the exact dialogue, but they make it pretty clear that this is the New EPA.
Besides, truckloads of episodes testify to the show’s eviro-credentials (see: the crazy Texas billionaire vs. various of Lisa’s dreamy do-gooder love interests). There’s really no chance they’d spend all that time contradicting themselves with the thing that millions more people are sure to see than the average episode.