They did the same with Enemy Territory.
In both cases, the game code is the bottle neck.
But as Carmack said, it was a consious decision, as they didn't want the game programmers to worry about parallelization. The game code programmers should only care about writing the code that makes the game fun.
The system programmers that does the hard core stuff like rendering, obstacle avoidance, collision detection and so on, they should handle the parallelization problems.
So I think that Carmack was talking about the game code, when he talked about using a scripting language.
Doom 4 will be build with the same model, so it is something he stands by, that the game code should be easy to write.