Really, the Hadron Accelerator (and the Mass Driver as well, though slightly less so) is overpowered. Its extremes of power simply don't fit in with Starfarer's mechanics. It's a guaranteed overload, and if not, it'll still deal a hearty amount of damage that allows you to fire from a safe range, all in a package the AI doesn't know how to deal with.
S'why I refuse to use those weapons. IFed ships are still fun, but the guns are just Too Good. Even the autoguns (mostly the light ones) are too efficient compared to other light kinetic solutions; low OP, high flux efficiency, high range, all with a burst fire that makes overloading a little easier. But at least that has the drawback of little raw dps.