Interesting. So you would expect it to work only if WebIDE is connected to the device? This is just for prototyping and debugging? And if you disconnect IDE you don't expect to have any alternative for the input?
It could work i similar way like the Graphics.dump() so that it could print some specific stuff to output that WebIDE would act upon and present a dialog and then trigger callback with the result via pasting some code into console (like e.g. setTimeout(callback,10)).
Maybe even some generic way that would call into WebIDE browser runtime so you could really call the real window.prompt() yourself and get the result via some callback.