I sure would try.
Try the diplomatic way first.
if does not work,
I would write a letter to manager of dealership with cc to Ford customer service.
Dunno ... how much money are we talking about ? Usually they charge less than $100 for a diagnostic. The diagnostic was kinda correct though, the guy found a fault in the charging system, I guess he was not very thorough in his diagnostic to determine the exact root of the problem (would have changed the alt like you did and found out the problem was the fuse and charged you for the alt anyway).
just my 2 cents,
iougs -
