I agree with that whole list of reasons why Alberto was the leader, and the favorite, and I can find you quotes of Bruyneel saying just that. Even saying most of the exact things you said.
Going into the start there may have a corner of his mind that needed to stay open to the possibility Lance might have the goods but that all went away after prologue.
http://www.bikeradar.com/news/article/contador-named-astanas-tour-leader-22177
Still talking out of both sides of your mouth. It's a nine man team. They are riding FOR someone. They are not just out there tooling around with a DS that doesn't know his **** from a whole in the ground. Tell me who you think they were riding for. If it was Lance it has to be AGAINST the interests of AC, which I'm going to respectfully disagree with.
I don't see any evidence that there was ever any strategy employed by Bruyneel that hurt AC's chance to win or that didn't maximize the chances that if something happened to AC another Astana rider, not even necessarily Lance, could contend, which is he gets paid the big bucks to do. I watched and re watched the same race you did.