From my use cases, I still can use my trackpad and keybaord that's part of my 15" MacBook Pro, but when I plug in my Thunderbolt Display the peripherals attached (Mouse & Keyboard) actually working is hit or miss. If it's not working I've had to hard reset my computer to get them to function again. Unplugging the Thunderbolt display and trying to plug it in again results in the computer acting as if the display was never unplugged to begin with (It's not mirrored, but extended display which I can't see at this point.)
I've tried putting the computer back to sleep and unplugging/replugging in devices. Just nothing that's hooked up to the Thunderbolt Display work. I also noticed that if I tried to play any videos that required rendering, that also didn't function (e.g. Netflix, Hulu, VLC).
Anywho, this hasn't worked for me since I've had the display, and none of the updates up to this point have resolved this issue.
Pro, Mac OS X (10.7.4), with Thunderbolt Display Attached