After his initial question, John remained quiet throughout the three beings' speech about the chaos the creature had tried to wreck, but it was a deceptive quiet, with his reactions to it easy to read in the frustrated tension of his body. What they had pronounced would save this world and the timeline Ruby hailed from (perhaps more, depending on what timeline theory was ascribed to), but it tied John's hands in regards to his family. Of course beings who fought on the dimensional level would have no concern for, or even understanding of, the issues that might not end the world but could still destroy fighters on one side of this war, but he did. The demon's damage had been thorough and now he was essentially told that if he did end her, she could return to Hell. From there she would no doubt once again find her way to the surface and finish the job with the Sam of that timeline.
Weighing the lives of others against his family was a position John had found himself in before, but it had never been the lives of all versus the lives of a family larger than his two sons. The only thing that could possibly be worse than being told he needed to let this demon live would have been living with them telling him he had to leave the YED alive. But even that was no comfort.
And then they threatened his kid. Torn between the overarching need to protect and a low-in-his-gut dismay that Sam appeared to be trying to hide behind Faith, John moved to close the distance between himself and where Sam and the beings were standing, but stopped a step and a half in as the idea was set aside to give Sam another chance. For that, John couldn't even feel the depth of gratitude that he wanted to feel, nothing more than a shallow victory, because he had no idea if this would just end as a delay of their action when Sam took this chance and ruined it with his powerlust and blood hunger.