Dedicated missile boats, yes. You can do that. The problem is that on ships which would ordinarily carry normal SC and have rockets, you can't do that. The only way to have them in the game now and have them work remotely correctly is to use SC on missile boats and just say that the missiles in capital ships are capable of evasive maneuvers or something.
I suppose you could use frigates instead, but whichever system you used would be ridiculous if you wanted to FF anything.