I think pass-through will work for you if entered early enough. I've discovered on Google Docs that if I manually enter passthough I still can't type, but if I reload the page with pass-through enabled things work.
You can take advantage of pentadactyl's :autocmd
feature to run the pass-through command automatically based upon a URL regex. For example, to disable pentadactyl on Google Docs you would enter the command
:autocmd LocationChange 'https://docs.google.com/*' :normal! <C-z>
You can make these changes permanent by saving these commands to your .pentadactylrc
file.