I should add that I have two missile specialized ships in Scy, but I had to give them huge drawbacks to keep them in line. And still, one of them is still a bit on the OP side. In my case it's the absence of non missile weapon (save 1-2 small slots for PD depending on witch ship), a 40% CR cost per deployment and a slow CR recovery. I think they are balanced when equipped with Scy missiles, but with pillums and ECCM it's not the case.
The point being: you can make a missile ship balanced, it just won't be a super fun/useful ship in the end.