Leave the key in the car and it won't do that annoying honk. It's honking to let you know you that you are leaving with the key while it's running. A common trick/bypass is to hold the key over the top of the windshield as you shut the door. It fools the computer into thinking the key is still there. From what I've read, the car will run for a good 15 minutes at least without the key in it, including if someone were to jump in it and steal it. They can get pretty far in 15 minutes. But then again, the FiST does have the #1 theft deterrent system in the country - manual transmission.
There is a fix for other Fords via the ForScan system but as of yet, nobody has figured out the code for our cars. I deliver Chinese food in mine and it drives me nuts. I won't leave the key in it because it has locked me out before. I just close the door slowly and partially. If you close it til it latches but doesn't fully close, you can walk away with the key and it running, without it doing the annoying honk. You can lock the doors with the lock button on the key, but you won't be able to lock it with the button on the door handle.
Hope this helps.