If your capo use causes your guitar to pull sharp you are not using the capo the right way.

Put the rubber pad on so the front edge presses the string onto the fret wire instead of between fret wires and boom, intonation problems disappear on a properly set up guitar.

Takes an extra second to place it, but very worth it. Try it yourself. I do this successfully with Kyser, Planet Waves and G 7th capos.