My problem is not that they're a threat, it's that I'm sick of fighting them. It takes hours to micromanage the targeting of 100+ FACs, especially the mopping up of the crippled ones, and there's no challenge since I've proven my ships can kill a matriarch and her entourage. I'd rather spend my time on precursors and NPRs where there's the possibility of a surprise and the possibility of gaining something.
I think I've cleaned up the last of them in my current game, though, so I'll just leave the box unchecked in my future games.