I have the same issue. Also on the 360.
I turned in the Helm of Winterhold after I first read about the glitch (unfortunately had killed some mobs in order to get it ... which evidently is a no-no) and hoped that would be enough. Nope.
I went ahead and cleared the entire dungeon, hoping the fragments would somehow be there (as supposedly the Silver Hand took off with them when I got back to town with the witches' heads).
Nope.
Now all of the Jorvaskr NPCs are perma-stuck with a bunch of looted Silver Hand bodies at their feet.
I have the witches heads and no way to revert to an earlier save (has been over-ridden long ago and way too far into other quest lines to even think about backtracking).
I'm willing to wait and let the dungeon reset if you think it'll remedy the problem.
However, if riding out the 30 days to let the dungeon reset doesn't do it, then what? Wait for the patch? But that won't fix any current character quest glitches, right? I really, really want to finish the Companions, being soo close to the end, and this is just ... grr. I would hope that since this is a main quest line, something so minor as killing a few mobs to get some helm won't break it, but ... it is what it is, I guess. Sigh.