HipHop expects the PHP source. You cannot remove the source files.
It is not a byte code compiler and should not be compared to Java's redistributable bytecode. HipHop is a runtime environment where PHP is JIT accelerated.
PHP is a dynamic typed language, so it's difficult to generate efficient machine code. HipHop observes the execution paths of PHP scripts over a period of time and makes a pretty good guess. You could turn on Authoritative mode, so that the file is read in once, and never expect to be changed. Even so, the JIT needs to be warmed up.
If you want to deliver a bytecode format of PHP, use a OpCache product instead of HHVM. But it's just not the same.