I'd much prefer game mechanics that encourage "good guy" players to buffing the AI.
You may prefer that, but it's ignorant (sorry) of the simple fact that if the game allows people to be "bad", then some are going to be bad, no matter how much the developer encourages being a "good guy". Which is problematic, because if that good guy doesn't shoot commanders too often, but murders security forces all the time to flip systems, are they a "good guy" or is that actually just as amoral?
So if we presume, rightly, that the game will allow amoral actions, regardless of any personal moral standing, or who might be impacted, how do you solve that?
Adequate application of the law. Given most people want system security levels to mean something, this makes high sec mean something, but equally, that will make anarchy mean something.
Which also means those who prefer to not be shot at, will stick to systems where that chance is reduced, and where there are adequate consequences for when it does.
And these CG's are in Anarchy systems, so no AI anyways.
Yep. So folks should have some understanding that flying into Anarchy systems is sketchy at best, with a heightened risk to person and ship. Getting salty because in a system that has no de facto security force (just loosely coupled paramilitary factions, for the most part) and why can't people be nice, again ignores the actual situation.
The game presenting amoral choices, where there are some places those amoral choices have lower consequences, isn't a fault of the game. A lot of games provide amoral choices. The only difference here, is people have a
preoccupation for expecting everyone else, to solve their problems for them. Rather than understanding that amoral choices have been included by design.
Again, it's important to remember
the developer has specifically marked these thargoid related systems as Anarchy. It's purposeful, intended design. So at some point, you might have to consider the notion that the
developer may have an amoral design goal, for the game.