Sorry to hear...It's pretty easy to slip and scratch the area round the 30way connector, even more so on the iPad 2 & 3 due to the rounded edge. Only thing you can do is be more careful.
I think what I would do is to stick a small suitable label over the scratched area having carefully cut out the hole to match, a discrete thin plastic label should'nt look too much out of place, perhaps one that says.. 'warning..easily scratched' ;-) at least it would prevent further scratching and hide the currrent scratches, or fit one of the proper thin rear protectors a suggested.