What people actually have a problem with isn't the specific code you took out, but with your whole attitude to the people playing the game and your mod as expressed in that code. I'm going to step around that, because the likelihood of you changing or improving is small, and just deal with this from a game design perspective.
You can't regulate the experience of other players (modders are not 'elevated' or 'exceptional' players; we're just fellow players) that closely. It's bad design. There's a lot of stuff out there that meshes badly with other mods, that's not well made, that makes the game trivially easier, and I have opinions about all of it. Sometimes I wish it didn't exist, sure, but it does.
The reason I don't try to police it with hostile code is because this is my hobby and I want it to be fun, not a war of all against all where we compete to try to make playing and modding the game less fun for our fellow players.
I'm pretty sure you designed the Legio for pretty much the same reason I added the Blade Breakers; to challenge the player. To throw something at them that was a cut above smashing your average fleet, that was unique and interesting. The problem is that you can't force someone to want the same kind of challenge you want, or force other mods into the design paradigm you'd personally most like to balance against.
Some players are always going to want a straightforward power fantasy where they effortlessly smash the opposition, and that's okay. Put it out of your mind. Design around the default experience you're presenting being a good one that makes you personally happy to work on, and let the rest of it go. Don't try to balance the entire game; just deal with your corner of it.
And seriously, get a therapist. We'd all appreciate it.