The Enemy

He was perfecting a medical discovery, The old General might need an operation

The story clearly states two reasons: Dr. Sadao was perfecting a discovery to render wounds entirely clean, and there was a possibility that the old General might need an operation, so Sadao was being kept in Japan for this purpose.

Tom

The American sailor reveals his name as Tom when he says impulsively, 'Anyway, let me tell you that my name is Tom.' Hana only responds with a distant bow, showing she doesn't want to get emotionally involved.

They feared harboring an enemy would bring trouble

The servants left because they believed it was wrong to help an enemy American. They felt that Dr. Sadao and Hana had forgotten to think of their own country first due to their long stay in America, and they feared the consequences of harboring an enemy.

True

True. Dr. Sadao performed surgery to remove the bullet from the American soldier's back, even though he was conflicted about helping an enemy. His medical training and oath as a doctor compelled him to save a life, regardless of nationality.