This would redeem Alexis completely. How I hope you're right!
I understand how you feel. Eugene is deeply hurt by Alexis' action. He dedicated his entire life in the new world to help Alexis avoid Alexis' cruel fate. Yet, Alexis immediately cut Eugene out the moment he found out that Eugene might be some sort of prophet. After having some time to think about it, Alexis is beginning to realize that what he did to Eugene is totally wrong and completely messed up. He regrets it greatly and is trying his best to earn Eugene's forgiveness. But even more than Eugene's forgiveness, he doesn't want to lose Eugene.
To Eugene, however, what Alexis did was more than just abandonment. He felt like Alexis betrayed him. Eugene has done more than just earned Alexis' trust. He's proved himself time and time again his devotion to Alexis. At the very least, he deserved the benefit of the doubt. But Alexis just ignored him and cast him out. This, to Eugene, will not be something that can easily be overlooked. Even though Eugene still loves Alexis and is considering to forgive Alexis, Alexis' action has solidify Eugene's resolve to cut all his ties to the new world in order to return to his old world once the new world is saved.
To simply put it, even though Eugene may forgive Alexis, he might not choose to stay. And I'm afraid this will cause Alexis to become the villain again like the original story. Cause more than forgiveness, Alexis wants Eugene to stay by his side. Should he learn that Eugene plans to return to Earth, Alexis might abandon the entire mission all together. Alexis will imprison Eugene against his will and keep Eugene from completing his mission in order to stop Eugene from leaving. He will go against the Male Lead and Female Lead and even the gods themselves if it means keeping Eugene by his side. This is something that he's completely capable of given his character so far.
I guess Alexis is beginning to realize that Eugene is ultimately tied to some sort of fate. And the only way for Eugene to be free is if the fate is fulfill. Even though Alexis hate prophet and fate, he loves Eugene too much to give up on him. So he will fulfill this fate in order to set Eugene free of this fate. That is why he's trying so hard to support Eugene's mission. But I think he also realize that even if he help Eugene fulfill this fate, that doesn't mean he and Eugene will be together afterwards. So he is desperately trying to keep Eugene by his side in fear of losing Eugene.