My opinion? Yes, I believe the US would side with Israel. The subject of intra-alliance conflict is not new and every alliance have this potential problem throughout history. Notably, the conflict between China and the Soviet Union, the world's communist leaders, that led to China coming to friendly terms with US via Nixon. But it is very easy to say that we would side with Israel -- blanketly. If it was that easy where the moral and social ties between the two countries give Israel some sort of license to do as please, then we would have seen far more conflicts in the ME than today.
Personally, I support Israel out of strategic considerations, not because I feel some sort of emotional bond with Israel. If Israel is clearly in the wrong, Israel should bear the consequences without America's intervention.