We need a lot more singular they! Even Shakespeare used they in singular. I think your translation this chapter is appropriate and fits Japanese pronouns and the context well without compromising either. After all, Japanese pronouns usually don't distinguish between gender. Even somewhat-gendered pronouns in Japanese can be stylistic and vary across personalities and eras (boku, watashi, especially the latter in formal use).
It's great having a centuries-old gender neutral pronoun, especially for me as a they/them enby. So it is a bit heartwarming to see you popularize a (very old) usage. I'm clear that Kou-kun identifies as a woman but pronouns are something else entirely.