I'm gonna take a stab at this. You didn't state the value of both fuses and my 2005 is probably different.
If the replacement fuse was rated higher than the original, more current will go through the wire before the fuse blows. Copper is expensive. In all types of electrical and electronic fields you use the smallest wire that will do the job. (With a small safety factor, say 10%).
Smaller wire is cheaper and doesn't weigh as much.
Did the wire get damaged due to being overloaded? I don't know without more information.
Go ahead an leave the new alternator in. I just replaced a 21 year old alternator. It decided to let me down at night and on the interstate.
Rebuild the old one and you'll have a reliable spare.
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2005 2.3L XL 5SOD 3.73 K&N
KYB Shocks Husky Toolbox
Alpine / Rockford Fosgate Sound
"Ask me about my AC Vent fix!"
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