I've spent far too much time looking for reasons and hidden meanings and motives and trying to understand what exactly the subtext was all about in His Last Vow, and have finally reached an astonishing conclusion - there are none. What we saw is what there was. Oh Mycroft no doubt had some Machiavellian plot to rescue his brother at the last moment, but other than that I am willing to believe that Sherlock really IS messed-up enough to accept that his best friend's wife's actions were quite acceptable in the circumstances, and that John is messed-up enough to forgive her.
Looking at the history of the show and the resolutions to the two previous cliffhangers. After eighteen months of OMG how will they escape from the pool we get Moriarty answering his phone then calmly walking out of the pool building. And after season two - all of that "Sherlock had to die to protect John, and Lestrade, and Mrs Hudson" only to find that Mycroft's men had taken care of the snipers, and that was not Sherlock's motivation at all.
Be interesting to see what season four brings us.