But you could quickly recover by hosting those JS files yourself and relinking them.
If your app is coupled tightly with AppEngine APIs, then there is nowhere else you can host your app.
What about your data? Most web applications have persistent data of some sort that is vital to the user experience -- without it, you don't have much of a site.
[Edit: And keeping a hot copy of that data is a lot harder than it sounds]
I don't think so. Javascript files hosted os s3 would hang the page loading and without css/images the app would be useless too.