The only thing I could see as a problem is if the player defending against a fighter loaded ship launches a Admin shuttle at the beginning of the mission at about range 60, then the defending player high tails towards the Fighter loaded ship in an arch.. this could draw the fighters off by 50+K from the intended target...
This is an exploit.. However, i could also see the Admin being used as an alternative to a sensor decoy that does not effect the main ship..
I can also see the counter to the Admin by Playing in F11 where everything shows up with distance and speed.. as soon as one sees an object moving spd 6, one could lock on to it with a LR weapon and blow it to pieces if one is in range with LR weapons.. for Fed, this would be Torps, for Hydran, this would be Hellbore, for ISC, this would be PPD, for Mirak and Klink this would be a High Speed Drone.. now this would take away from some of the Heavy Weapon capability of the fighter launching ship for a short time, but it is doable...
also, using the fighter Control panel a bit more should allow you to put the fighters into Defend me mode to keep them in close, and then re-assign Attack mode when you have the main enemy ship targeted.. yes this takes time, but it should re-orientent the fighters to their principal target...
Either way, there are ways to overcome the effect.. the races I can see at a disadvantage would be Lyr, Gorn, and Rom...