So while trying to resolve an issue in FRED, I've stumbled across this. Apparently ordering a wingman, a wing or all fighters to "Disarm my target" or "Disable my target" will make allied warships refuse to engage said target. Just now I also discovered that ordering my pilot(s) to disarm enemy fighters will also make those enemies not targeted by the allied warship.
Here's a video of some testing I have done. There's more detailed text in the video itself.