Are there really military organizations like ATLAS from cod advanced warfare?

You mean are there really out there PMC's that are the equivalent to Cobra? What do you think?

How quick do you think an ATLAS employ got in his letter of resignation after coming into work one day and finding out that his company has threatened the world with Chemical Weapons, attacked a US carrier, killed US troops with said chemical weapons and has set up their very own Auschwitz outside of Baghdad?

No.