A couple of problems with that approach are that
1) Just cause I`ve disabled a bomber doesn`t mean that it still shouldn`t shoot at me with its turrets.
2) Fighters with engines down should still shoot at you when you get into their line of sight.
3) You have to write a change-iff for EVERY ship you want disabled. Like I said it's not too bad for a wing or two but if you want to have a mission where you have to disable 6 or 7 wings they you`re going to need an awful lot of SEXP's.
4) When dealing with Terran or Vasudan opponents a disabled ship is still a threat cause they could be repaired by a supply ship (I know we never actually SEE one but the NTF and HOL must have had them)

Having an enemy supply ship jump in and start repairing the disabled fighters was a twist I did originally consider having but decided against cause it was too much hassle for too little reward. On another mission though it could be a lot of fun

That said when dealing with Humans or Terrans you can say they`ve surrendered. Doesn`t work so well for Shivans though.