Right now I find it easiest to let the marauders clear out the planet, then they will all group up in a nice tight circle. One lightning warhead can kill about 250 of them. The largest group I have seen attack a planet was ~300 Dagger Frigates.
Excellent point there -- you've inspired a change for the next version:
-Starships, marauders, golems and resistance fighters will now patrol around at random if they are AI-controlled and without any targets to attack. This makes them less predictable, and keeps them from "clumping" and thus becoming easy targets for area damage attacks.
Thanks! That should actually make those a lot more interesting to deal with (Starships included).
One more thing you might look at. Since the marauder frigates are missile units, you can send in units that are immune to missiles and kill them all while they just sit there. I have used Eye Bots, it takes forever, but it does work.
I don't know what to suggest here, but it seems like they should do something besides sit there and wait to die.
Maybe once marauders have cleared a planet, they should start to leave. However make it take just as long for them to leave as it takes for them to arrive, and if any targets for them come into the system then they will return if they haven't left completely yet.
The description for the marauders says they come to collect what scrap they can, but leaving all your ships there to die eventually doesn't seem like a good way to collect the scrap...
This way you can either wait a good long while for them to leave again, or you can go in and fight them to clear out your planet faster. They would be more of a hit and run enemy.