That sucks! I'd be pissed,too. They removed the factory coating inside that prevents corrosion ! No,not ruined,but still that was not very professional on their part. I'd give it a good sanding with some very fine sand paper if it were me.Provided you have enough to spare.
Also,that outer o-ring is just a dust seal.It'll be just fine. Although it doesn't look it,powder coat is actually a very thin coating compared to actual paint. It won't interfere with your seal at all.No worries there bud.