They'll take out anything that's armed. If you attack them, they will proceed to destroy anything of yours that isn't armed, too. This is how the event works; it's just worded wrong.
A long long time ago on normal difficulty, I ran into a Peacekeeper event that can only be described as a plague. Fleets of 15-20 huge hull ships sporting 400 attack/1400 defense (I forget which of which but at that point does it really even matter anymore?), for a grand total of up to 8000 attack/28000 defense per fleet.
It really didn't help that I was >500,000,000BC in debt at the time, either.
I suppose it wasn't as bad as it could've been-no AI could fight them, as they had matched their defenses to them, and I had no ships, so the only things I lost were a few...heavily upgraded and fortified...mining starbases...
But then I had to build something to take them down, and that was the hard part.