I'd point out the scratch and hardball the seller down. And yes, they'd come down. Or I'd walk... unless this is a tough coin to find.
i can't say that I disagree with your logic, but I just have a different way of thinking. Slabs, and grading in general, are not pertainent to my collecting. I am assembling a type set and for the most part collect coins that have an appealing look, regardless of grade. Many of the coins I have were in slabs when I got them but were broken out soon thereafter. I'm not anal about grade or condition; as long as the coin looks good I'll take it. I have very few coins that were graded less than XF+ and many are MS with defects. I just picked up two slabbed coins this weekend - an AU55 1854 Half Dime and a MS60 1864 No L Indian w/damage -and each have a date with the hacksaw soon. For now, everything I have is in 2x2 holders in a three ring binder and this suits me just fine.
I went through a whole bottle of Slab Renew. When I needed more I bought PlastX and saved a lot. It's just as good. Only downside is that spots on the rag dry white with PlastX and are hard to see (Slab Renew is tan). Use a colored t-shirt with PlastX. I seriously doubt you will be able to polish out the scratch you describe. Probably much too deep. NGC slabs can be especially difficult to polish. I would probably bite the bullet and pay to have it reholdered. Sure, the coin's undamaged but the scratch will always be there, annoying you. Photos may be tough too. Lance.
As a general rule, deep scratches will be problematic, but roughened areas (that appear translucent white) come off easily. You can also use the PlastX to make your car's headlight covers like new -- forget that expensive stuff they try and sell you on TV.
Get the PlastX -- it's cheap and worth a try. If that doesn't help, and you're in no rush, wait for next Baltimore show and submit in person. If you're in a rush, send to NGC for reholder. I think that's your best course of action, if doing something about the scratch is something important to you. IMO, of course.
Slab Renew and PlastX will not fix a cut in the slab. Both products can not go that deep sorry but that slab is gone just as if it were cracked.