I just finished rewatching the series, and more times than any other character, Marshall is usually the voice of reason, but what the hell was up with him in that season.
Seriously, yes the way Lily handled the San Francisco situatation terriblely back in season 1, but you know what that was before they were married and before they had a kid and she has more than paid her dues for those events. She has been supporting Marshall since the show began, keeping her clearly unfulfilling job so that he can follow his dreams, whenever he quits his well paying jobs to work environmental, despite any financial situation they might be in, which he does at least twice.
They made the choice to move to italy for lily's dream as a family and he made a choice for his dream on his own. He was in the wrong and he knows he is wrong, why do you think he goes to so much trouble to stop lily from finding out and to stop them from talking about it when she does find out. Bringing up San Francisco was just a cheap shot.
Also in the end he does choose to let her follow her dream, but his main reasoning for it is just connected to another one of his dreams of having more kids.