I notice that, in a sense, AWS proves that the Total Cost of Ownership of Windows infrastructures is higher than the TCO of Linux infrastructures.

Amazon charges more for Windows instances across their entire offering. A Windows micro instance costs 50% more than a Linux micro instance ($.03/hr vs $.02/hr). This likely reflects Amazon's statistical studies on their EC2 datacenters that a Windows stack (OS + apps) uses on average more resources than a Linux stack, therefore more power costs, cooling costs, etc.