I just read your post and it got my mind going. I think you're on to something here, and I have somewhat of a theory of why this feature was removed from the control panel.
I have an ATIV 700T and A 500T and am fully aware and annoyed by this problem. It seems it was addressed for recent versions of One-Note (I use 2007). Just yesterday l had a chat with someone who owned a Surface Pro and bought it with all the gimmicks
including the latest Office and you cannot use your hand as an input device on One Note there unless you manually activate the feature.
I guess the marketing strategy here is to get people investing on new versions/subscriptions of Office as opposed to giving all users a general solution in the control panel. Inefficiency is a profitable thing sometimes.
But even if this is true, Microsoft is the only company willing to offer digitizer technology on devices with full operating systems. Guessing by the many times my ATIV has been compared to iPads/Android tablets or even MacBook Airs, I'm thinking that
at least 95% of the population on Earth can't even wrap their heads around what this thread is about. That's a tiny market, so I'll stay thankful at this company for having these options available to us at all... for now.
In the meantime, here's a link to a solution I found that has worked for me. It gives the option to enable/disable touch without restarting your computer. It's still not perfect (you won't have the touch option to scroll and have to target the scroll bar
with your pen instead which is annoying), and it needs you to hunt on device manager for the proper command for your device on initial setup, but it seems to be the best fix out there at the time.
http://answers.microsoft.com/en-us/windows/forum/windows_8-hardware/how-do-i-disable-touch-when-using-wacom/6fcd772e-d48a-4203-b754-6a3a11887baf
Hope this helps anyone.