there are solutions used to fill the scratches, which as far as i know are mostly used for car related stuff. Most things that are for computer-related-stuff are cheap crap used to remove scratches from CDs DVDs etc. which is basically some chemical used to eat away a layer of plastic, thus removing the scratched layer and making it look all neat and not scratched. You'll have to hope someone has experience with this, as i gave up trying to find a decent product for under 20bucks...
then again the vita screen has a coating, as most phone screens etc. i'd think, to make it smooth and lovely to touch, so polishing out the scratch will likely ruins that and you'll get a sort of odd spot to touch on the screen.
I'd recommend applying the screen protector, if the scratch isn't deep/large it will mask over it mostly and will be a fair bit less work...
google gorilla glass scratch repair for more info on the topic as there posts in other forums i dont want to get slapper for linking to. good luck with that.
