Yes, the whole David thing is quite intriguing. Of course one might argue that they are playing the scene with Sherlock for the fun of it, showing how serious Sherlock takes his task and how he goes about it in his typical fashion. But his position at this very table is quite conspicuous. 

And of course there is his outward similarity to John, a means the creators also employ with Mr Holmes/John and Sherlock/Tom. I am sure that this is no coincidence. 

And there is the question why Mary needed a shoulder to cry on when she is so happy with John. Because I take it that David offered his support when she was already in a relationship with John. Had it been before his time, Sherlockw would not have bothered with threatening David. 

I thought the "shoulder to cry on" thing might have taken place before John, when some other relationship ended...but now we know Mary didn't have time for a lot of relationships as Mary. On the other hand she hasn't known right from the start of when she changed her name. 

But it's a good point that Sherlock wouldn't have acted the way he did with David if he hadn't viewed him as a possible threat to John. The speculation has been raised about Mary's baby not being John's. That would certainly be a convenient way to get Mary and the baby out of the picture...but I wonder if, if Sherlock knew that, would he have been so protective of Mary and the baby?

I think Sherlock would be angrier with a woman for betraying John than for hiding her past as an assassin! Or, more selfishly, he might take advantage of the fact to get her out of John's life. Conversely, if the baby is John's, Sherlock might have strong feelings about it which explain why he protects Mary in spite of everything else...this baby is part someone he loves, and he doesn't seem to mind kids in general either, judging by his relationship with Archie.