Something we can't rule out is the possibility of another group or rather, path. If I remember correctly, the MC can express not wanting to be controlled by HERO to his friends, and they agree with him (mostly Alice, I think), but they need to get stronger if they ever have hopes of getting under HERO's thumb.
I'd love to be able to fight against Ella and her goons and HERO via our own path where we ultimately decide our own fate and everyone else's, which it seems like Weird has laid down at least the idea of in the future.
We also have Jared's dad and whatever the heck he has going on with his group (although a lot of whatever he has is from Ella so it's probably all compromised if he ever considered wielding it against her).
I do wonder what the MC would do if they defeated Ella and HERO, lots of possibilities depending on the corruption/morality.
Probably that's the path the story is gonna follow considering everything that happened so far, MC and his superhuman squad against both HERO and Ella for greater justice, while the higher monster threat takes a backseat while this little war happens only to return in full force after the winner has been decided. Unless the dev decide to go multiple routes Devil Survivor style and make a path for HERO, for Ella and for Independent, which I highly doubt. Perhaps in the very end we might have some choice depending on corruption/morality like you mentioned and who is still alive after the final fight.
Yeah Jared's dad is mostly just one more pawn for Ella to use, I don't think he can act on his own without her knowing and allowing him to. She has been manipulating so many people for so long that I wouldn't be surprised if she ends up hijacking Jared's dad group like she did with the prime minister office when she still had Jake under her.