I feel bad for bringing this topic back from the dead, but I just saw the episode for the first time and read all the controversy around it. I have mixed feeling about it. I know Seth is a smart man, and not the most ignorant person either. He expressed that the trans community would really enjoy the episode which didn't turn out so hot.
I think this is because in his mind, all the really stupid reactions like calling Ida "it", throwing away the crumble, etc. are supposed to really stupid and over-the-top showing how cringeworthy, idiotic, and immature some people actually feel about transpeople. Unfortunately, satire isn't for everyone especially when the general audience is incredibly ignorant of the issue being satirized, which is this case is transphobia. Ida herself is shown as a strong woman, she herself is never actually portrayed in a joking manner and is actually admirable. So for anyone smart enough to understand that the Griffin's family reaction is meant to be disgusting because transphobia is disgusting, it's positive.
However, the masses aren't that bright and many will see this as justification of making transphobic jokes and being as non-PC as possible to fight the system or whatever the hell they do to protest "Political Correctness". Even Seth himself is a bit backwards because he said in any interview that cismen discovering they've had sex with a transwoman should be a unsettling thing. When obviously it shouldn't, but it just goes to show how much more a struggle we as transpeople have in the realms of awareness and understanding.