How do I disable the windows key when in-game?

For Starcraft II specifically there's actually an in-game option to disable windows key and/or alt-tab. It's under "Gameplay" the 2nd and 3rd last options.

Also for SC2 if you set the graphics setting to "Windowed (Fullscreen)" it will let you instant-alt-tab. It says it may cause a drop in performance but I personally haven't noticed it and the ability to alt-tab instantly is worth any small performance drop unless you're on a really low end system. (I browse the web when searching for matches, and just have "Play in background" turned on for the sound so I can hear when one is found).

Microsoft Support Article KB216893 How to disable the keyboard Windows key

Alternatively, you can use AutoHotkey to disable hotkeys globaly or selectively, based on the program that is currently active. This should work for any program, and any key (combination) out there.

This certainly isn't a general answer, but some keyboards (usually the fairly expensive gaming keyboards, like the G15) have a physical switch that will disable the Windows key.