Wait so what is this about, why they wanted to kill him ? Because he's someone westerner o...

Both. There was a period in history where Japan fought with "western" countries. And Christians, as usual, took advantage of war to try to convert other countries and people they deemed heathens. So they sent missionaries to Japan.

I think he might be a mixed raced actual bastard. So that is why they abuse or want him dead. And the missionary was trying to protect him. So whoever was after the boy, killed the missionary. So now the villagers are blaming the boy.