Lewis wasn't particularly far back (3-4 seconds maybe?) from Sainz, so double stacking them would have put Sainz at risk of being jumped during the pits, and then put Leclerc at risk from someone who wasn't his teammate in second place. They could have pitted Leclerc and left Sainz out and then tried to swap, but you're then basically screwing Sainz and also again risking a challenge from someone else.
He said "the first car that
wasn't Lewis". You're correct that Lewis wasn't far back (1.4 seconds), but even if Lewis had jumped Sainz, I very much doubt that he would have kept him behind him on the straights. We all saw how much trouble Leclerc gave Lewis, even with a broken end plate and on old hard tyres, so I'm pretty sure that Sainz would have gotten past Lewis in the event that they got jumped in the pits. That said, I don't think that a double stack would have been too much of an issue regardless as Charles was nearly 5 seconds up the road from Carlos at the time of the safety car.
As for Binotto saying that if they pitted Charles he could have come out fourth if others had not pitted....how exactly? Perez was 31 seconds behind at that point. The man is inept.