How does your hand hurt from stretching just 1 set of strings? You mean the treble strings since they are thinner/"sharper" feeling? If you had that problem in a tech setting I'm sure gloves would be an easy solution.

Not sure if there are any better ways, but I assumed the hand method was the best. I always did wonder about that though. Especially on a Floyd Rose set-up since those things can go out of tune easily and screw up your sound.