If he discovers the truth, the end of the world will inevitably follow.
On the day that Cipher let the twins know about his fate, they were naturally concerned.
If the end of the world truly came to fruition, there was no way for anyone to survive, and that included him.
Thus, in order to protect him, they had to prevent the end of the world.
And the only way of doing that was to prevent him from discovering the truth.
However, as he had told them, he would stop at nothing to find out said truth.
If they stopped him, they knew.
The resentment, the disgust, the feeling of betrayal.
Neither he nor they would ever be able to recover if they stabbed him in the back like that, especially after he opened his heart and revealed everything to the two of them.
But, if they weighed it alongside the alternative on a scale, they knew it was the only answer.