I can't speak for anything other than the films I saw last year, but the audience was great - we all saved our incredulous chatter until the very end! I've never seen a big franchise film like Eva or whatever in the cinema so I don't know how SLA's audience reacts to anything with a bigger following. The screenings at the BFI have always had good audiences, too - but then, British cinema etiquette is, I believe, much more restrained than that of the US in general.
I have an idea of what you're talking about - when I was a student I ran my university's anime society, and we had a huge problem with people MST3k-ing their way through everything, no matter how good or bad it was. I think at something like the Madoka movies when you've got a critical mass of geekdom, the combination of sharing something you love with a large audience plus all that social awkwardness turns into something quite hideous