Their relationship does seem to want to evolve beyond friendship - it sort of feels like it has a life of its own. I keep coming back to that moment in TGG when Sherlock rips the bomb vest from John and then flings it away from him. The last bomb that went off took out part of the building and killed over a dozen people. Putting a few more yards between John and the vest isn't really doing to do anything more for his physical safety, Sherlock. It just strikes me as such a purely emotional, instinctual, irrational moment for Sherlock.