Find a decent independent mechanic and get a second opinion. Generally dealerships are an expensive choice for service once the warranty is up.
In this situation, the dealer simply is not being truthful.
If it is the PCM, rockauto.com has rebuilt ones for $200 plus shipping and core charges.
However, imho you need to find a good, honest and competent independent mechanic with experience in late model Ford electronics, and get a second opinion. Without additional information, there are many situations which result in a no-start situation. I suggest to ask friends and family where they take their older cars.
If that does not pan out, approach a local Mustang enthusiast club in your area and see who they can recommend. Here is a link for one which just might be nearby.
http://upstatemustangclub.net/