You only have to take damage if you get hit, it makes contact, or you try and defend against it.
If you have the potential to escape then you can, though most people use pretty wide range attacks when they've charged so much, which makes escaping pretty difficult. I don't know if Khan's character has the ability to eat away the ground or whatever, but if he does it's a more than legitimate escape for an attack which relies on floaty elemental damage.
Getting creative would have been the better option, I like to see charges like characters special abilities in fighting games. They're OP as fuck, but if you unleash them willy-nilly on a character completely prepared for them they just get blocked. It's all in the set-up.