If you happen to come across Khan, use the environment to your advantage. Get hits from a distance, run around, and get more hits on him. His relatively small shield lets you get more shots at him, too.
Khan is usually only a threat to the backline when he has his ultimate. Stay behind or inside your Frontline's shield to prolong or avoid Khan's ultimate completely as he cannot grab anyone behind a Shield.
Khan can prevent Fernando from protecting his allies with Commander's Grab. It will cancel his shield and displace Fernando behind Khan, meaning he must waste his Charge ability if he wants to be back in the fight.