These are very fair conversation points. Lily's character itself in the way it is written may just be a stand-alone deal breaker for some players. When I play the game, myself, I may just have to kind of 'go around her' character as much as possible as what you describe may be exactly the way the studio looks at it and if this type of content is so deeply ingrained and interwoven in her character and backstory then it's quite possible that no amount of options or switches will ever be able to address her character without borderline deleting her.
Somewhat tongue in cheek, but this brings me back to another post from a few days ago, and I can't remember the poster's name who had mentioned having the possibility of kicking her from the ship when that stuff is mentioned, but it would be a comical resolution for vanilla players that I'd absolutely choose if available - boot her from the ship, you lose her sniper special fire ability both in space and on the ground and then at that point Captain has to hit the battlefield himself and build his own army without mantic units.

THAT could be the branching option. That or they could actually consider putting in an option where you can outright reject one of the girls for reasons like this and from that point forward that character is not romanceable and is almost like a 'bro'.