Mozilla's problem with NaCl is that Mozilla believes in open access to the web for everyone, while NaCl at the moment is tied to particular hardware architectures. The two seem to be fundamentally incompatible.
If PNaCl ever happens, that might change the situation, maybe.
As far as legacy code, emscripten unlocks it as well. Not with the performance of NaCl (and unlikely to get there), but it has the benefit of running cross-browser right now and not forcing people onto particular hardware platforms.
And copying "valuable IP" out of an emscripten-compiled program is just as easy as copying it out of a binary, of course.
If PNaCl ever happens, that might change the situation, maybe.
As far as legacy code, emscripten unlocks it as well. Not with the performance of NaCl (and unlikely to get there), but it has the benefit of running cross-browser right now and not forcing people onto particular hardware platforms.
And copying "valuable IP" out of an emscripten-compiled program is just as easy as copying it out of a binary, of course.