Sherlock doesn’t want her to because only John can be John. He’s irreplaceable.
But it’s also the fact that he’s being honest and tells her to be herself rather than hiding it. John is his John and Molly is his Molly.
This scene is about Sherlock and Molly. Not everything is about John, or Sherlock and John.
The most important part of this scene is that Sherlock actually considers her to be important. He wants her to be herself, wants to know her. This is something we’ve really only ever seen with his best friend John, and definitely shows that the relationship between Sherlock and Molly has strengthened and deepened