Yes, it wears on the chains, but it's done 90% of the time at the crags. That doesn't make it right, but it's common practice. Most sport climbers lead, clip to chains, thread rope through chains, re-tie, then get lowered and clean.
It is even expained in some instruction books, specifically, I think John Long's Advanced Rock Climbing.
Rapping the chains is best on the anchors. I don't always rap, I re-tie and lower because it's faster or sometimes easier. Top-Roping the chains is very bad, but I bet 90% of the people here have done it or still do it from time to time. I see it EVERY time I got toa popular crag. I've seen people on this site do it. I've done it too.
I agree, i have seen this done, plenty of times at the crags. I am guilty of it myself. I am not saying its right, but most of the sport climbers I know just lower off. Now if you dont believe this, well!! I dont do it anymore =)