Jeeze, it is hard to make factual judgements, but I will share my thoughts. I doubt any post you get will help you financially, but it may help you detect BS if you see or smell it.
The shop that did your brakes was obviously incompitent if they turned rotors below minimum thickness. This says alot about them. If you took it to the local Brakes-R-us instead of a reputable shop, shame on you. One of the two shops is obviously not reputable. Pick up one bad rotor and have it measured by a third shop (this is so simple, they should not charge you anything), and now you know who you can trust. Stop doing business with the liar immediately, even if they offer to fix their mistake for free. Brakes are important to you (and me)!
One reason for a minimum thickness on rotors is there needs to be a certain mass of metal to absorb the frictional energy of braking. Too thin and they overheat and warp too. If they overheat, it can transfer heat to you caliper and harden the rubber seals in the caliper. I don't know why it happend to the rear, since the front does most of the work. Maybe they were already old and this agravated the problem. Also, maybe the the heat "boiled" the brakes fluid causing air and loss of braking. You would have to be doing some pretty hard braking, even with the thin rotor condition to cause this problem.
Another posibility is that the calipers are old, gunked up and dragging, which is causing premature brake wear. In this case, the original shop should have noticed this as well, but was not caused by them.
So, you need to do some more research with the shop to really understand what they have found wrong, not just what part is bad.