At this point if Apollon wanted to finish off Archanfel he could, but there was a scene that indicates he wouldn't (yes JP, I'm trying to make you buy the manga for this, MWAHAHAHA!)
Also, Barcus said Apollon's armor is made of the same material as a Guyver's Control Metal. That was a possible hint at Apollon being a Creator, or agent of the Creators.