Will it won't be the original paint job either way... I say paint it whatever color you like best. It's your car, and the damage is already done since it's not the original as is...
I love the wolfgang sealant. I asked this same kind of question a lot of people recommended the PB stuff. But in the end I looked at a bunch of pictures of cars with WG vs PB and liked the WG look. Haven't tried the PB but i love the WG!
Back when I owned my mustang it had a spot that looked kind of like that. It was tree sap that had stayed on the car a long time before I removed it. I was left with some pretty ugly spots.