If it really bothers you, you can get a scraper from Brownells (www.brownells.com) that will allow you to deepen the disconnector notch, which is really the safe way to do it. You should not shorten your disconnector. Polishing is OK, though.
I'm having a disconnector "click" problem; doesn't altering the disconnector slot negatively affect the disconnector function? The disconnector should, at the slightest rearward movement of the slide, disconnect the trigger from the sear; if you deepen or lengthen the slot, aren't you increasing the distance that the slide will have to travel, and increase the possibility of firing out of battery?