Before we knew for sure that Vaughn was alive, I watched the episode "Prophet Five" so many times to find clues!
Here is what I gathered.
After Vaughn had been operated on and was in the recovery room, Sydney went in to him. Then Jack walked into the room and reported to the two of them that Gordon Dean was a bad guy. Jack and Sydney were each standing on each side of Vaughn and Sydney said to them, "What are we going to do?" It then cut to a commercial and then Sydney fed Vaughn the drink, he flatlined etc.
So my theory is that after Sydney said "what are we going to do?" the three of them decided that the only way to keep Vaughn alive was to fake his death so that Prophet Five would believe they had succeeded.