I have successfully removed scratches from a number of Citizen crystals using a set of diamond paste syringes from eBay, and a Dremel with a soft polishing mop. Takes about 10 minutes tops - allow an extra 5 minutes if the scratch is deep. .
Something like this would do the job >>>
http://www.ebay.co.uk/itm/RDGTOOLS-2...5iLndFOfmPMSjQ
Don't let it get overheated which could damage the glass. Spread the polishing area around a bit to avoid visible distortions. You don't need the Dremel, but it is very slow to do it by hand. Other brands of rotary tool are available and you can use a cordless drill as an alternative. Easier to clamp the drill in place and offer the watch to the polishing mop rather than wave the drill around! Use masking tape to cover any metal areas that you don't want to polish. Sounds far more difficult than it is.
Good luck