Sherlock and John weren’t a unit in TBB.  They didn’t work beautifully.  Sherlock didn’t expect John to run after him into danger, and John didn’t trust Sherlock to handle trouble alone.  Because of this miscommunication, Sherlock runs after Zhi Zhu, John follows for absolutely no benefit, and Soo Lin dies.  Because they acted like individuals, and not a team, people suffered.

They will never do this again.  They will have plans, they will talk to each other, they will trust each other.  They will never again leave a victim alone.  By HLV, they are in sync.  Sherlock knows that he can’t run off without telling John to stay put, and John trusts him to handle the danger upstairs while he tends to Janine.

Mary knows all of this.  She knows how they work.  She’s heard countless stories about Sherlock from John, and she’s seen them work together.  She knows that if there is a victim, John won’t leave them.  Because she knows what happened the last time he did.  

Mary left a wounded Janine to tie up John downstairs, and confirmed it with Sherlock before shooting him.  Because she knows all of their weaknesses and how exactly to exploit them.