I think a better way to represent Fed fighters is to have them fly CAP arround your ship. Make the squadron behave like the new vulcan ship's little supprt craft, it hangs arround your ship (or maybe an ally's you designate) and defend it by shooting down mines, incoming enemy fighters, heavy torpedoes, and engaging enemy ships that get too close, but always staying arround the ship they're escorting and not flying off chasing something.
I think limiting such fighter squadrons to one per ship would be fairly reasonble. Make it obtainable as a rear weapon slot or as a console (sci would be my guess). The console would allow for Photonic Fighters and would calm down anyone that feels Escorts should not get fighters (an arbitrary p.o.v. since Star Trek follows so few realism guidelines anyway, why not let escorts in on the fun?).