Many people seriously don't understand Hajime's character. He said it clearly when he met Yue that he doesn't care about the revenge anymore and the only thing he's trying to achieve is getting back home. Killing Hiyama won't help him find the way to go back to Japan so he doesn't bother. And he doesn't see Hiyama (or even Kouki, for that matter) as a threat to him, so letting them be wouldn't hurt him in any way.
Also, don't need to tag me for spoiler about Hiyama; I also read the LN, thank you.