If I recall, Otomo Sorin, the head of Otomo Clan at this time, converted to Catholicism. Maybe in this timeline, they are firmly in Organtino's clutches...
As for Hanbei, it might be TBC, considering his usual depictions. Or if it's anything like Sengoku Komachi, measles.
Killing is still acceptable in the context of war.
Also. There's the simple explanation to the lie that beef is still a luxury meat and poor European peasants simply ate cheaper meats. The cow ploughs your field. The cow gives milk. Cows are expensive. They only eat cows which are too old to produce. Poor folk wouldn't think of beef as a childhood meal.
Saint Ignatius wasn't talking about conquering lands, but souls through conversion. The battle is the one between good and evil, between ignorance of God and knowledge of the way to be saved.
The Black Legend of the Jesuit is, quite obviously, a legend.