Few things here.
1) Red wing fighters (or at least some of them) are guardianed, but their engines (and possibly weapons, didn't check) aren't. Which makes no point whatsoever in guardianing the ship in the first place.
2) I think I noticed red wing fire heavy missiles at fighters.
3) Not really your fault here, but red wing is utterly incapable of firing their missiles correctly at subsystems if you give them any order overriding their mission-defined orders. Which makes micromanaging a pain in the arse. But I blame the AI.