Maybe the large squads should split into two wings if possible (if they're mission is fighter sweep or something, sweep two different areas.) If a large squad is given an attack mission, why not let them divide some to attack and some to escort (especially if you're over 12 people in the squad, 8 bombers, 4 escorts.) That way you don't have to assign an additional squad as escort. Also, you could ask a large squad on escort duty to cover two attack squadrons.
Overall, numbers would still be messed up, but maybe you wouldn't run into 3 v 1 fights.