If you look at this HTML5/WebGL minecraft engine, it stutters even without any other players or bots in the environment.
Meanwhile Minecraft running in Java is smooth on even the slowest machines.
Benchmarks indicate that Javascript is 4x slower than Java.
http://j15r.com/blog/2013/07/05/Box2d_Addendum
The alternatives like ASM.js and PNACL are far from usable. ASM.js has no support for threads and PNACL is unlikely to be supported outside of Chrome. They also have no debugging support.