I've taken it out during relic hunting for the title, both at the slightly powerful stage with 4 cap ships and a bunch of good frigates and cruisers, and at the incredibly powerful stage, with 16 capital ships, and a fleet worth 2000 (maximum). With heavy casualties. Unless going for relics or suchlike, theres not much point in getting them. I mean, its only an income of 7 and you can't build any logistics (though they make handy novalith cannon platforms)
I would say that on small and medium maps, and certainly in multiplayer, theres no need in taking them down. And in huge maps? Unless you're somehow untouchable, theres no need either. If you're fed up with them attacking, a novalith cannon is handy for taking them out from a distance, or the vasari weapon. Pity I play the advent now ^^. Then again, I imagine that a fleet with a mothership with "malice" could take them down pretty fast.