No the PATS system cannot be eliminated
If the Theft Light is flashing when you try to start the car, then the PATS device is not recognizing the Key. If you only have one Key, then you will need to have Ford or Locksmith connect Scan Tool & Reprogram the Key to a "Master Key".If you have 2 or more Keys, try one of them first.
You can try this also:
Disconnect the Negative Battery cable for apprx. 5 minutes.Reconnect the BatteryLock and ulock the door with the remote or key.Turn Ignition Switch to the run position just before Start (crank)If the Theft Light stops flashing then start the vehicle. If it still flashes then leave the key on for at least 10 minutes. Then try to start. If it fails to start then both key/s will have to be reprogrammed.Be sure to have the Key/s programmed to "Master Key"