If web gaming becomes a thing I think people should start thinking about a standard way to let people rebind their keys, through the browser or some common library.
On the rare occasion I still write in German, I use OS X' fantastic compose key feature: ⌥u makes two dots and any following key is then converted to an Umlaut, so ⌥u + u = ü, ⌥u + A = Ä.
Writing the scripts is ugly, but effective and not too tough
I've yet to find a reasonably good Linux clone of AHK, but then, most Linux games I've encountered tend to be quite configurable. Starbound comes to mind as problematic, but I haven't touched it in a few months.
In any case, QWERTY is not the default worldwide. The letters 'a', 'w', 'e', 'd', 'z', and 'x' have no special semantic significance for this game, they're chosen for their relative positions in a particular keyboard layout.
The actual game actions of 'shift upper left', 'shift upper right', and so on, should be able to be associated with any particular input - including other keys, or relevant swipe gestures on mobile.
I agree with OP - there should be a standardized way of doing this, so that game authors don't have to re-invent keybindings for every new game. (or, as they're wont to do, fail to re-invent keybindings)
But you are effectively changing the input method from "typing" to "gaming", so it makes sense to have to toggle some switch somewhere.
Actually, Javascript is a little weird with regard to scancodes. Try playing with http://javascript.info/tutorial/keyboard-events in different keyboard layouts - you'll notice that there's no code that's consistent across different layouts.