If the js is written by someone else using GWT and is therefore
obfuscated then good luck!
But if you're writing your own GWT app and you know you're going to
want to hook into it using javascript for whatever reason... not sure
why you would... but you should use GWT's JSNI which is a way of
getting the GWT compiler to output some handwritten js code. This is
handy for primitive implemenations for things like js to flash
bridges, etc (although I'm working on a GWT wrapper for the entire
actionscript language if anyone is interested?)