Stelios believes that Helios is young, naive, and easily impressionable. His worldview must have turned upside down because of the betrayal and that made him do what he did. He doesn't have any other reasonable explanation for why Helios betrayed the plane. The possibility that Helios is a clone or might be related to the hidden god and the demon didn't cross his mind at all.
Helios can't possibly be someone else's clone because he was there the day Helios was delivered as a baby and he has watched that baby grow up every day of its life. Clones are not born like babies, they are made and they resemble their creator in every way. Helios never came into contact with knowledge about demon summoning nor did he come in contact with shady characters.
