DMUpdater DOES have the option to go completely back to stock. I've never tried it, so I don't know how well it works, but that's what I used to root, so if I decided to go back to stock, I'd use it to do that as well. From everything I've read, those guys really know wtf they're doing. I couldn't believe how easy the rooting process was with dmupdater. This will root, are you sure you want to? really sure? downloading. Open back up, creates recovery for you.
Again, not sure how the unroot works.
On a side note, not to be insensitive, but is there any way you can get us some pics of the damage? I'm always interested to see what they look like after horrible accidents. I can't believe mine hasn't shattered. I've dropped it on the hard tile floor at work 2-3 and the battery cover has fallen off and battery flew out almost every time. The tile is some kinda stone, so it's like effing concrete!
Not sure how it'd work if you DIDN'T go back to stock...I mean, if you took it to a vzw store and they saw that you had it rooted, they could deny your claim, but if you're sending it in to them after they've already sent you a replacement and you've paid the fee, idk if they'd even bother to check the software stuff out. I imagine they'd just flash it back to COMPLETE stock with no extra apps or anything and fix the physical damage if it's just the screen and/or a few scratches that're messed up...