If Mykage is Elder Johannes it sort of makes sense he killed Jin.
If besides Celiane, Fudo was instrumental in Apollonius defecting to the Human side he wont let him do it a second time.
Also it was payback for Futaba as Fudo did nothing to save him.
Speaking of Futaba I think I may have figured out why Amata has wings for his feet.
As seen here Apollo wasn't just a reincarnation of that universe's Apollonius but also the reincarnation of OVA Apollo. Same applies to Silvia and Reika.
Theory:
So while Amata and Kagura may be reincarnations of Apollo, part of them is the reincarnation of Futaba.
It would explain certain things. Amata's angel wings and Kagura's child-like temperament.
Mikono and Zessica given some of their doubting personalities perhaps both has Silvia and Reika's souls in them.
Remember Mikono felt she should ask Kagura's forgiveness. Silvia already asked Apollo, Sirius and Touma to forgive her... But she can't ask Futaba's forgiveness as he was dead.
Futaba was a child killed by the New UN for their Assault Aquarion program.