Even if Windows were running on bare hardware I could play tricks with the clock, I could hide memory from any program that Blizzard could come up with to attempt to scan regions of memory, I still could pull all of the tricks you just mentioned. How? Using good ol' virtualisation extensions that exist within processors.
Not only that but I own the hardware, I have physical access to the hardware, there is no good way for any program to insert itself at a higher level. I control the boot process so I get to choose where the OS is loaded, I get to change the way it works and interacts. Writing kernel level modules that tamper with time like you are suggesting that would be simple with Wine are entirely possible using straight Windows as well.
Thats the biggest problem, Blizzard doesn't own, they don't manufacture and they can't guarantee that no-one has tampered with the hardware. There comes a point where the software is running on top of the hardware and it has to trust that the hardware is not being malicious. This is how cable box hacks, and satellite box hacks used to work.
Blizzard can write a root kit all they want, if people want to cheat and if there is enough incentive to do so people will find ways to defeat the rootkits behaviour and cheat. Until everything is sent over an RDP like protocol and no code executes client side this is a problem that is going to exist for the foreseeable future.