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.

Flank seris and use your ult at the start of a fight to ban her twice, leaving her team without heals for 8 seconds

You can actually challenge Makoa, because you can ult to execute him, as he does not become untargetable to your ult while in ancient rage.

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.