Either Sherlock following John was part of Irene’s plan, or she didn’t think it through very well.

Sherlock was standing at the window, composing. He watched John get into a sleek, black car, and probably instantly called Mycroft to demand why he was kidnapping John, again. As soon as Mycroft told him that he wasn’t behind John being whisked off, of course Sherlock would have followed.

And even if Sherlock hadn’t been at the window watching, it’s assumed that Sherlock has 221 under surveillance. He would have seen what happened and informed Sherlock immediately.

It makes that entire conversation that much more powerful and meaningful, doesn’t it?