Where was your dog sitting? I screwed my dog up, which was the same as your's. My dog wasn't the least bit gunshy, but I muzzle blasted her in training a couple of times not even thinking about it. Make sure the dog is sitting behind the muzzle and barrel, not next to it.
As for correcting the problem that may have been created, it just takes time. I know my dog is not scared of the noise of a gun, because I can still shoot over her in the upland field, but my dog is scared of the situation of sitting at heel, saying mark, and then pulling the gun up. She knows that her ears have been rang by this before. I tried going back to the shotgun and just pumping it as a fake shot, it wasn't really going to smooth though. Right now, the decision I made was to give up on duck hunting her this year, because I don't want to force her into it, I want her in the end to enjoy it. She is only going to be 2 in Dec so there is plenty of time to hunt over her in the future.
What have you done since the incident? Whatever you do, don't force the dog into having the gun go off. If you don't think the problem is bad, go back to a cap gun and throw some fun bumpers. Just make sure you're not holding the gun on her ear level. I see alot of guys do this. Then work up to the shotgun at a distance, maybe even hold the shotgun and do what I mentioned above. It really depends on how serious you think the problem is. Let us know how it's going and possibly some more info.
"Because a duck is just a 3 pound critter"