Will there be a story line where you can make a choice if the MC stays good, or turns evil? Like instead of working against the Hegemony, what if she/he decides to actually join them and turn the Inana into a space happy harem? Or how about the Hegemony discovering the MC's treachery, and do it themselves? Any possibilities of either scenario?
Don't think there is much chance of turning the Inanna into an actual harem and joining the Hegemony properly.
MC isn't really in charge, they are just playing a role. If it looks like the MC is turning she already said what she'd do to him and the crew are loyal to her, the captain that is.
Possible for the Hegemony to do it themselves after discovering treachery but then the MC would be dead so that would be a game over.
It already has 2 branching paths with various things going on in those, i'm not sure if another huge branching path would be worth it considering how much work games take it would put back updates even further.
I suppose they could revisit it at a later date and add in a third branch, like an evil DLC or something.