I tried looking for an answer to this but didnt find it, so forgive me if its there, but when the peacekeepers showed up, they wiped EVERYTHING out that they could find, regardless if it was within the borders of my space, as the little pause screen said i was good if my ships were in my space. What happened?
Hmmm...I don't know. When I got the PK event, they left alone unarmed ships so freighters were OK to move around, but massacared anything armed. Then they retreated to a few lonely corners of the galaxy and just sat there waiting for someone to come and pick them off.
I don't really know if either way they operated is correct, but there is my experience. Kryo seemed to indicate that what they did to you was what they were intended to do.
About the logistics thing, just build up some fleets of cheap throw-aways and keep throwing them at the PKs until they die...I had to do that with a fleet of superpoweered pirates before. Think of it as a good mechanic to help you modernize your forces