It shouldn't be hard at all. Just change the programming to stop allowing Windows to override user specified settings - ever.
Of course, they are unlikely to ever give up that power... :D
Honestly, the checkbox should have another state. NEVER show the task bar unless I hit the Windows button. Ever. It messes up so many things on your desktop, hides crucial application buttons, etc. I'd much rather have to intentionally hit the Windoze button to bring it up than EVER see that nuisance bar when I don't want it.