Look, I get it, you want to take care of enemy balance first, but if you want to do that and get more info from the player, you just need to ask them! Like, just go around the comments asking them about, or even better, why don't you make a survey for us to fill out? A survey every update or so would actually be the perfect gauge for a lot of things in the game, not just enemy difficulty.
Now, you said that if you put a difficulty option in now, 'a good chunk of people would just give up at the first sign of challenge and switch to easy', if that actually happens at some point in the future, the problem wouldn't be on the players giving up and switching to easy, it would be the thing that's causing them to do that!
Speaking of that, I think that the real problem isn't even enemy balance at this point, it's the combat! Like I already said before here in the comments, the combat is just dogshit, and I really don't mean that as an offense. The defensive buildings have no damage numbers and no range number anywhere, so the player doesn't really know what they do, it's just like Spacethumper 1 but with more enemies and defensive buildings, and in my view a sequel should be an improvement upon the first game, not more of the same...