FYI, my experience...
I was rooted stock LI3 with CWM 5.5.0.4 installed... the clearing Google Services Framework trick finally worked and I got the OTA at about 2am this morning... I just let it download but didn't try to install it (knew it would fail)
I ran Voodoo OTA RootKeeper first to save root, then pulled the zip from cache, copied to SD card and rebooted to recovery... figured I'd try to install from CWM straight-up and it failed as expected (failed signature verification error)
I had a hunch so I rebooted and enabled everything I had disabled previously (via normal Android application manager)... thing is, and I'm 99% sure this was the key, I also had a few of them that I had to freeze (but not remove) via Titanium since they couldn't be disabled normally... I think the update script is smart enough to notice apps that were disabled that normally can't be and throw up due to it... so, I also went into TI and defrosted those few as well
Rebooted to CWM and installed from SD and the update worked fine... no data wiped or anything like that, everything as it should be but with JB goodness! Oh yeah, and RootKeeper did its thing perfectly, restored rooted afterwards no problem.
So now I just have to go disable all the "cruft" again and I'm good to go
Oops, just noticed though that it DID restore stock recovert... so not *quite* perfect I guess... but hey, easy enough to reinstall CWM so no biggie. Call me happy