The scene in question had a girl named Sugar who claimed that she had "self-diagnosed Asperger Syndrome" and could therefore say whatever she wanted. She then proceeded to be a complete bitch, and also the only character on the show thus far who can't sing.
A lot of people are saying that because she says it's "self-diagnosed" it's okay because the show isn't actually making fun of people who really do have Asperger Syndrome. But as someone who actually has Asperger's myself I can say that no, it is not okay. It still perpetuates the negative stereotype of "Oh, Asperger's doesn't exist, it's just an excuse people use to act bitchy and mean to people". Which couldn't be farther from the truth, by the way.
Asperger's is already incredibly misunderstood enough as it is. A show like Glee, which is supposed to be about tolerance and embracing diversity, could have used their platform to increase people's understanding of it. Instead, they chose to play it for laughs, in a way that wasn't even remotely funny. It doesn't help that a lot of people who watched the show missed the "self-diagnosed" part of the line and thought Sugar was representing people with actual Asperger's. Or that part of being an Aspie involves often missing social cues, so other people on the Autism spectrum who watched the show may have taken it at face value.
I really don't see how Glee can redeem itself after this, unless the writers make a public apology for going completely against the message of the show and excluding a group of people for the sake of making a cheap joke.