Having tried a similar thing to "disable" Windows hold on the WIN key, I found that there wasn't a way to disable all of them - only a few.
However, Autohotkey can override windows hotkeys, as you've found.
If you just want to disable Windows' use of those keys (if I'm understanding you correctly), you could try something like this:
F11::
F12::
return
That would effectively disable the use of F11 and F12 anywhere as long as the script was running.
(no, trailing spaces don't make any difference)