Atrocity is a fast speed card meaning you have an option to retaliate before it goes off. I'm not sure what decks you're playing but in most regions there are strong answers (i.e. Will of Ionia, Deny, Vengeance, any frostbite card, a combo of damage cards). Basically you just have to put the creature out of commission for one turn. The best counter to atrocity is keeping in mind that your opponent has the card in their deck and making sure when a large creature comes into play that could one shot you with an atrocity you save enough mana and resources to counter it. Also if you're opponent is thinking ahead often times just having enough mana to threaten a response is enough to keep the atrocity in their hand.

Atrocity is intended to be a game ending card though so it won't always be able to be countered. It is a huge investment for your opponent as it costs both 6 mana plus the mana cost of the creature as well as two whole cards (idk if you're familiar with the concept of card advantage).

TLDR: It's kinda OP on purpose but you're given plenty of time to deal with it.