If your holster has scratched the pistol, it will do it again and again unless you cover up whatever was scratching it.
If the marks are in fact scratches, or gouges that go into the metal, you might be able to use some contact cement to put some thin leather over what you refer to as scratches.
However, if the marks are simply deposits of brass onto the stainless steel because brass is softer than the steel, the previous suggestions of Flitz would be worth a try. Because brass is a soft metal similar to copper, you might try using a strong copper remover such as Sweet's 7.62 bore cleaner.. Sweet's is a strong ammonia based bore cleaner that will dissolve copper and/or brass deposits in a rifle bore. If the marks on your slide are deposits of brass rather than scratches that have cut into the stainless, Sweet's should do a great job of removing them.
I would start with Sweet's or a similar bore cleaner that is designed to dissolve copper deposits. If you polish with Flitz and a Dremel type tool before trying to dissolve what is a brass deposit rather than a scratch, you might end up with a more highly polished area on your slide that wouldn't match the rest of the slide.
Once you begin polishing a part of the slide, you run the chance of being in an endless cycle of trying to always keep the flats of the slide "pristine" and chasing after every little scratch, and brass or copper deposit. First find out if it is a scratch or just a deposit of brass.
ETA: I re-read your initial post, and you said the plastic scratched the stainless. There would need to be some thing harder than the stainless in order to scratch it, and steel is harder than plastic. I suspect there was some kind of grit or dirt inside the holster that caused the scratch.