You could try running a stanley blade over the area to make it smooth and some of the metal might chip out,
The sooner you do it the better as you have found out once it starts to rust you can see it, and make the marks far more noticeable. Usually using a sharp blade gets it off and then use some rubbing compound to get the rust marks off.
It's happened to me several times over the years when welding or grinding near glass even when covered with a dust sheet the little molten marbles get through.
It happened to a mate of mine once when cutting through some angle iron with a 9" angle grinder near his Mum's double glazed back door
Left a nice big grey racing stripe up the glass