IIRC the game emulates a CPU (either 8 or 16 bit can't remember), which means that at a basic level the binaries and source will be the same thing since the only language supplied with the game will be a form of assembler.

Of course we can expect people will create compilers (I believe some already have) to compile other languages down to the assembly used in the game.

The viruses/trojans will be an interesting thing, I believe notch said that it will be up to players to protect themselves from these.

There's a risk here though for essentially turing complete griefing, so hopefully there will be something to help protect newbies from accidentally running some horrible code.