These were once fortress cities that guarded the most highly navigated (and obviously highly policed) trade routes
Taking them will not be so easy...and of course, they are so dis-repaired that there is not much left to take, even if you succeeded in stabilizing their alien systems, could you even use them?
Remember, the mechanical devices embedded into the now dead organics are not like your basic computers...and neither are the now "rogue" weapons, the computer interfaces and controls are all written in Laminari, and spoken in Laminari...a now 'very dead' language amongst such persons as yourselves.
You might end up blowing yourselves up
Of course, even the Laminari cannot enter the perimeter very easily at all, the Rogue guns target us as well.
What organics that remain are what helps to power the systems, and transfer energy and commands like living nerves. EMP will not do much to harm their systems, deep in the santuary-cores of these fortresses.
They are prime hazards in the deep forgotten reaches of old, once charted, but now lost space.
Few come across them...or live to tell about it. Hidden in deep clouded nebulae, wrapped in fields of ice, or bathed in the scarlet shadows of dying suns...
To come across one of these Laminari graves, is to come across the abode of the Angels of Death themselves.
And those armed with protector-drones are even more dangerous. Ships that escape the hundreds of gun batteries are pursued in a near endless, and disparate hunt, as their damaged ships are sent engine-screaming, 'Death driven' into the vast empty blackness of open space surrounded by plagues of these merciless, mechanical guardians like mangled flies around the last vestiges of a piece of rotten fruit. Jumping in and out of real-space taking bites out of the doomed ship's hulls with their organo-metal bodies, or their ancient, mysterious weaponry.
They are graveyards friends...disturb not the dust that lingers there.