"proprietary" is a spectrum, not a binary decision.

You can be open-source, documented (though NaCl is not so documented in practice because of the Pepper dependencies), published, and encouraged to adopt, but if your development is controlled completely by a single company and if you depend on other, undocumented, parts of that company's software stack, then you are more proprietary than something with an open (as in, developed in the open, with many participants) standard and no dependencies on a particular implementation.

Obviously you'd be less proprietary than, say, ActiveX, but that's a pretty low bar nowadays. NaCl is not competing against ActiveX; it's competing against the web platform as it exists. And that's definitely much less proprietary than NaCl.