Loosing him would kill Sherlock.
She had seen it. Seen the way that they had unintentionally melded. They revolved around each other so blindly it was a wonder they didn't crash.
Whilst walking they'd be almost shoulder to shoulder. On a crime scene not even a meter would separate them. They had gotten so bloody comfortable with each other that they could bounce ideas off of one another without saying more than 5 words.
It was a far cry from the socially inept Sherlock Holmes she had once worked with. He still was that person, don't get her wrong. But now he had his doctor to act as a buffer between him and the outside world.
She didn't know whether to praise the lord or try to kill him. Because in the end, John wouldn't be able to keep up with Sherlock. And when that happens losing him will kill Sherlock. And she is not sure that she wants to know what a heartbroken Sherlock Holmes can do.
So she endures it, watches from afar the ever tightening bond, dreading the day that it will inevitably snap. All things must pass and she anticipates what Holmes is capable of.
But seeing Sherlock die before John.
She should have gotten her priorities straight.
It was easy to forget that John was a skilled Doctor who had once belonged to the army.
Looking at the four linked assassins to Sherlock's case all slumped over one another in a pile on the office floor, she truly felt fear.
Because she had anticipated what Sherlock Holmes was capable of if he ever snapped.
She had never accounted for what the unassuming Doctor could do.