In general, scratches caused by the action of wiper blades can be removed. However, in very severe cases, even if possible, it would be inadvisable to do so.
Scratches caused by wiper blades do not come from the rubber, but from either the metal arms, or contamination such as dirt, rocks, or other miscellaneous debris.
The usual marring of glass by wiper blade action is light and can be completely removed.
If the damage is deep, removing enough glass to for the window wipers to contact the glass fully would be inadvisable.