I am not familiar with the 1.6L engine, but I assume it uses a standard Ford alternator.
It sounds to me like the inside of the bolt hole on the alternator has a buildup of corrosion that is preventing the threads from coming through.
Since you have already backed the bolt out enough for all the threads to clear, I think if you just find a way to pry straight out on the bolt head, it will come out.
Some penetrating oil might loosen up the corrosion a little and make the job easier.
Good luck!