I think that you can try to bring your car to an independent service specialist and ask them to have a look at the rotors. Probably it only need some resurfacing.
I have about 30K km on my GS, and do not have any problems. I think that the Lexus hour rate is is relatively expensive, en resurfacing is not a 100% garantuee, so that is why they do not offer this.
In general the brake rotors will outlast 3- 4 sets of pads.