Since the key-less entry system operates via wireless signals without physical contact to the ignition system.... You may be able to use tinfoil to cover the key so that the signal that the key puts out may not be boosted.
The key-less systems seem very similar to RFID cards if not the same. I think that they have RFID technology in Europe for awhile now. They make wallets that have a tinfoil lining that block RFID signals.
Amazon has Key-fob protectors and this website sells them as well.
You can also make your own key-fob signal protector. This article below is more suitable for storage in a house or apartment setting or something else.
The fob-guards are more mobile.
With this setup you may not have to disable the key-less entry system. You would have to take the key out of the key-fob guard when you want to use the key-less entry feature.
I suggest consulting with a Ford dealer if this setup shall work or if they have any recommendations.
There is talk of a electronic chip that is in the works that will tell how far the key is really from the vehicle to counter the signal boosters. The chip would signal that the key is really this far and would not listen to the signal booster. I think the chip functions like a radar or a Lojack system to tell the distance.