Great behind the scenes piece as usual. I loved it. Don't get me wrong. But speculating that MI6 had him killed, on other parts of the piece, just doesn't add up for so many reasons. The first being the you give them too much credit, both in having the means and even a plan.
Your main point, which I couldn't agree more with, is that Putin does not benefit with him dying. If Putin really wanted him dead he would have been dead a long time ago. My guess is signals were crossed and someone did the wrong thing. Beat him too hard. Shoot him. They may have even forgot to open the door and he froze outside.