To get the update:
I got my wife's droid 2 working after it had been rooted. When I had rooted it using Z4Root, I changed the apps that I didn't want running originally to .bak.
I used ES File Explorer to change all of the file extensions from .bak to .apk. You have to give ES File Explorer R/W access to start this.
After changing them back to .apk, I unrooted the phone using Z4Root.
After the reboot and unrooting the phone, I was able to get the update and install it... worked great.
If you used Titanium Backup to freeze the apps you didn't want running after rooting, unfreeze them and then unroot your phone with Z4Root. This should also work.
Now to reroot:
Use the DROID 3 Root to reroot your phone after the update. You can then rename the files that you don't want running back to .bak with ES File Explorer or use Titanium Backup to refreeze them.