Is the sound subtle or life disrupting?
If it's subtle then I'd leave it, most throwout bearings make noise as they age, especially if they're on the cheap end. You're out of powertrain warranty so I wouldn't expect Toyota to do anything for you, but it is a known issue. Leave it until the noise becomes more present and worrying. Throwout bearings rarely fail catastrophically, if yours was suspect it probably would have given out long ago.
http://www.ft86club.com/forums/showthread.php?t=52176
http://www.ft86club.com/forums/showthread.php?t=96974
http://www.ft86club.com/forums/showthread.php?t=98247
http://www.ft86club.com/forums/showthread.php?t=21676
That's just what showed up in the first 4 google results, there's dozens more posts about it.
Edit: As above, squeaky pedal is a lack of lubrication, proper lubrication may involve the same amount of labor as replacing the throwout bearing requiring removal of the tranny.
7 hours is kind of a lot for a transmission removal from a professional shop, but it's not totally out of the ordinary.