There is actually a tool for straightening disc,
The DT-2 is specially designed and precisely manufactured to gently adjust bent or damaged brake rotors. Laser cut from high quality steel.
www.parktool.com
I just use a small cresent wrench to straighten my discs
There is a good video out by park tool on how to straighten discs and many other videos by others.
Basically ya straighten the disc while it's on the bike.
First number the spokes of the disc so you can keep track of where it's bent
Then using the tool or a wrench ya bend the disc in or out where it's bent until you get it straight
It's easier than it sounds with a little common sense of which way and where to bend the disc