The thing is, creating unique stories is difficult. Because it is inevitable that out there someone has created a similar idea. A century ago.
So, what you do is accept that fact and put your personal spin on things. And yes, its also possible this storyline in EA is just a throw together. I've been in other EA games where the EA story had nothing to do with the real plot of the game.
Would be nice if they'd clarify, and if there were more options.
I don't see siding with Mindflayers being an option, especially since until you realize something is different about your tadpole, you're led to understand that it will kill you. Even then, there is concern that its just a slower process and you're still in danger of becoming a mind munching monster.
There's no way to put a positive spin on that outside of lying to you and not letting you know that you're undergoing ceremorphosis. This would of course fall apart the second you realized that they pulled a con job on you. And why persuade you to help them when they can just throw you in a cage and do it forcefully?
The only way I could see mortals allying with the illithid is corrupt nobles in a city based setting, conspiring to trade over the entire town to the illithid. Which would make you the BAD GUY of course.