Having said that they are still Ahl al kitab and fall under dimmah (protected, second class citizen) status in an Islamic state; genociding them certainly isn’t acceptable.

Wrong. Jews are enemies of Islam and their status wont save them from death as long as they remain enemies of Islam.

But, he recognized the wretchedness of the Jews

Doesn’t matter. He hated Jews because of their race/blood, i.e. he hated Bani Israel. To hate all Bani Israel is certainly kufar because that would mean one hates many Prophets as well.

To hate kuffar is not to hate the messengers of allah. The rasouls were muslims and bringers of the word of allah and they have nothing to do with jews as a people.

You are clearly uneducated on the matter. Its perfectly halal to clean the disease that is Israelis from this world.

The prophet aws himself said that arabs were the lowest and most despicable of humanity before Islam (and they are when they abandon Islam).