A 2009 with only 12k miles on it? That's also a problem!
As I see it, there's three common ways to wear out a rear rotor. Normal use high mileage, lots of dirt/mud riding or you're a tail dragger. Riders who start out in the dirt tend to use the rear brakes a lot on the street. Now I'm not looking to start a "how to ride" thread nor am I saying I'm all that, but you really don't need your rear brake on the pavement. It has little effect anyway. My F8 has 45k kms on it with the original pads and rotor that's barely worn. It's been to Alaska and back so it's far from being a poser. The front brakes have two discs and four pads which are a lot more effective for stopping and wear better. Not saying your a bad rider but take note of how much you use the rear.
To answer another question, the rotors have a minimum spec for a reason. If the rotor is thin AND the pads are really worn then you run the risk of blowing a puck and possibly locking the wheel. Rotors are often run past the limit but with thick pads. Under 4 mm is a bit excessive though, not worth the risk but YMMV.
I've seen riders trade in their bike with shot rear brakes then bring their new bike (different model) shortly after and have the same complaint. Problem follows the rider.