The rear takedown pin goes through when the upper is off the lower, correct?
That being the case, I'd just dremel out the hole on the upper until the pin will go through to the other side. One of those small round sanding drums or a rat-tail file will do the trick.
Place the upper on the lower with the front pin out and you should be able to eyeball where material needs removed. Failing that, just look inside the hole on the tab of the upper, you should be able to see where it's rubbing/scraping.
You may have to sand/file a bit off the sides of the tab on the upper it it's too tight to close on the lower, too. You should be able to see where it's rubbing and just take it down a little bit at a time until it fits snugly.
That way all of the removal is on the inside and out of sight. Touch it up with a black sharpie if it bothers you and you're good to go.
The oil from the lube on your BCG will keep anything from corroding.
**I've had to do this on a couple of builds. Usually they're juuuuust off enough to put the pin in a bind. I wouldn't widen out the holes on the lower at all, ever.