I did not see an SPN episode called “Scarecrow” where "Sam leaves Dean (again)" (paraphrase of common fannish description, not an exact quote from anyone).
I saw an SPN episode called “Scarecrow” where Sam and Dean parted course on an unpleasant note because they couldn’t agree on whether to go to California or follow John’s orders. Later, they spoke on the phone and exchanged apologies, and Dean in particular apologized for having called Sam a selfish bastard and said he admired Sam for standing up to John.
At the end of the episode, Sam chose to put his mission aside in order to be with Dean. Dean, in the meantime, did not deviate from his goal, choosing to stay his course rather than reunite with Sam.
Characterizing this as Sam leaving Dean “again” requires taking Dean's perspective to the point of completely distorting reality.
During their fight that leads to the separation, Dean refers to Sam as a "selfish bastard". This insult is in part a reference to the fact that Sam chooses to pursue his own goals rather than saving lives, but that's not Dean's primary point. That's not the focus of their argument (and in fact, while this is not Sam's primary motivation, it's possible that Sam joining their father to track the demon would also save lives). After calling Sam a "selfish bastard", Dean says, "You just do whatever you want. Don’t care what anybody thinks." That's not about Sam letting people die.
The criticism of Sam for doing what he wants despite what other people think is on the surface a criticism of Sam for not being a good son to John. But it also carries the implication that Sam doesn’t care about his family at all—including and specifically Dean. Their argument in Scarecrow is Sam not wanting to do what Dean wants to do - and in Dean's heart this is a betrayal of Dean. Whereas Dean not wanting to do what Sam wants to do is not at all a betrayal.
When he apologizes later, Dean starts says that he wishes he himself could stand up to their father. Dean, consciously or not, looks at himself as the victim here. To turn on John, ultimately, is to turn on Dean. Sam fighting with John is a betrayal to Dean. Dean's emotions re-write the story, turning a disagreement between the two of them into an act of abandonment by Sam. He re-writes the story so much that Sam comes back and few viewers - and possibly not even Sam and Dean themselves - see that Sam has compromised and Dean has not. Sam was ultimately right to come back, this time. But he did not leave Dean. They left each other.
This re-interpretation of an event that we actually see on the screen supports my interpretation of events that are off-screen. Specifically, Sam and Dean's estrangement after Sam leaves for Stanford. I don't think Sam left Dean. I think John kicked Sam out and Dean, forced to choose between his two strong-willed family members, chose John and withdrew from Sam. But Dean, in his head (and likely subconsciously), re-wrote the story into Sam abandoning the family. And that's the interpretation a large chunk of fandom accepts.