At the start of each round, you can use your first setback at her, sending her way back and having her walk across a big path without any movement ability. If she plays Mother's Grace, act quickly, before she goes into cc immune state.
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.