This just seems like a definition dispute. "Stupid" and "crazy" are not precise words, so taboo "stupid", "smart", "crazy". Well, he's clearly not saying "most people have a low IQ". As timtyler pointed out elsewhere, this version of "stupid" is inherently relative. Eliezer's message is more like "most people make objectively bad decisions". If that's how you define stupidity, then I'd conclude that he is indeed saying that most people are systematically stupid.

"Stupid" isn't a very useful term in this focused a context.