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Once you obfuscate the JavaScript code, its actually a similar situation to that with Java or even regular C++ programs to a lesser extent, because you can still 'hack it up'. Look at all of the mods for Minecraft, for example.

Not true. You can't really obfuscate JavaScript in a meaningful manner without making it slower.

What? Take a look at Google Closure Compiler - it renames all identifiers to nonsense, making it impossible to work with, and not affecting performance at all.

And that obfuscation is easily undone:

www.google.com/search?q=javascript+deobfuscator

Clients can be hacked anyways, whether compiled or not. This has always been true. The only way to make a game secure is to keep all the game logic and data server-side. This means clients only act as dumb terminals: they provide input to the servers, and render the output.

Any network system that relies on the integrity of the client to maintain security is fundementally broken.