I think the bigger idea is that Simpsons is trying to be more representative of the social norms in the United States, for better or worse. In US culture, the outsider is always punished, regardless of intelligence. In traditional US culture, the independent intelligent woman is looked upon largely as the “old maid” of ages past, having a very limited societal fit.

I don’t think anyone wants to shun people like Lisa, but that’s always what societies have done. The greatest inventors have often been punished, whether by not fitting in, not being understood, or causing hardship by upending the power structures of the elites.

Society is and has constantly been more concerned with continuity, than progress. Not my preference, but certainly my perception.