Crowd control reduction or immunity is critical against Atlas, especially if you are a tank or support. This will make you less vulnerable to his Rewind effect, and reduce the time you are trapped by his ultimate.
Atlas is high damage tank very dangerous on solo fight. He can undo all dmg he has dealt for quite a while. He also can cancel all healing (self and from others) you've gained. To counter him you should always be with an ally to put pressure on him.
When playing healer in high rank games, try to hide behind cover immediately when Atlas ults, as smart players will banish the enemy healer, sometimes twice for 8s without healing your team!
Watch out for his ability to leave behind an explosive fissure, and stay away from it! This would result in him getting healed and you taking severe damage. Make sure to track him too, so as soon as he is physical you can attack and kill him.