When Khan tries to grab you, rewind him. When Khan ults you off the stage, use setback. You can even rewind him after he battle shouts to take away the heal. And with that, you've taken away Khan's best abilities.
Atlas is actually a great counter to Khan, as he can setback khan after battle shout, has a better shield and can rewind after being thrown out of the map. The main thing is to time your abilities correctly.