I can't at all explain why this happened, but my 11 Lexus GS350 warped front rotors and all I ever do is keep the car in gear and use the engine to slow down. There is even a Standard Simulation mode that allows me to downshift. I've used this method to nearly completely stop the car while driving around town. I only hit the brakes if there is a car directly behind me that needs to see brake lights to avoid slamming into me. Even then, I use downshift method to slow down. Not sure how this works as it is an Automatic, but seems downshifting does in fact allow the engine to mimic a manual transmission. It is a pretty cool feature that most cars seem to have these days. I use my A/C almost exclusively, so I'm doubting fuel efficiency is at all increased when doing this slow-down method. So, can someone please explain to me how OEM rotors warped at less than 30K miles and plenty of brakes still on pads?!
I would bet the problem is not that the rotors are warped (this really doesn't happen all that often). The problem is probably that after hard braking and then a sudden stop without release for a period of time, there is a small buildup of brake friction material which has embedded itself upon the surface of the rotor. This gives you a pulsating feeling when you try to stop.
This could correct itself if you were to utilize the brakes more often. It would ultimately clean the disks back off, giving a clean flush surface. If it is bothering you too much, you can always take the rotors down and have them turned slightly, which would clean up the surface. At that point, if you have good friction material left on your pads, you could continue to use them, but you'd need to make sure you bed the pads properly in the fresh surface, or you'll end up with the same problem again.
There are many different ways to bed the brakes. Normally I will bring the car up to 30mph and stop hard, slowing down to 10mph but never stopping completely. Do this three or four times. Then you need to let the brakes cool down. After that, take the car back out again and do the same from 50mph. The key part here is while you are running and doing the hard stops, do not stop all the way. This will leave the brake material on the rotor and you'll be in the same shape you were before. Also, when you go to park the car to let the brakes cool after the first run, only use the brakes as lightly as possible, trying to allow the pads to rest on the rotors for as little time as possible.