That aaid, one of the more interesting debates I participated in at Sun was Bill Joy's insistence that interpreted Java would be "faster than C++." From what I recall of his argument, it was that understanding the semantics of the program and just in time compilation would allow the JVM to run only the code that was needed in a smaller resident set with fewer context switches. At the time I was arguing against that, saying that a compiled version of Java could be a useful systems language but the interpreted version would not.
And even with some really really amazing hotspot technology on the JIT compiler, I don't think Java was ever faster outside of a few synthetic test cases that did no useful work.
So it really doesn't surprise me that a C++ version of minecraft would out perform a Java version, but it would be much more interesting if they included a JVM for the mods, so that the core was fast and the mods were portable.