Well just in time that 5000 contest of SCP just finished and the winner which is now SCP-5000 is hinted that: this SCP-682 is inside people's mind and those who know about this fact will feel disgusted about human so much that the SCP foundation decides to kill every human
That's one theory yeah (unless the author confirmed it to be true).
The other being that there is something inherently wrong with humanity, with humans. Finding out what it is leads to the same extreme disgust that 682 harbored for the last decades, leading to the Foundation deciding that genocide was the better option.