I am sorely, sorely tempted to agree with the idea that you should call people out because of this completely sexist attitude. But I'm not sure that's going to be the best thing to do in every circumstance.
The thing is, the point of the "interesting assumption" line is to shut down a line of conversation, because it's inappropriate. So as much as I agree with everyone who says that this is a horribly sexist attitude (and it so is), telling anyone that, or even hinting at it, is going to extend the conversation.
So if you're okay having the conversation turn to gender roles in society or wherever else it may lead, then I think it's fine to say, "Hmm, that's an interesting assumption. I bet people wouldn't make the same one if it were Katie at home with the baby!"
However, if you just want to stop talking about it, I think a much better way to respond is, "Katie and Sean are doing what works best for their family, same as anyone else."