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.
But also they certainly were mocking Ted Kennedy with the Mayor of Springfield.