Hmm, interesting. I don't find much that I disagree with in your message, so either I didn't communicate well (likely) or your disagreement is not in an area that I considered to be central to the article.
I think it is a promising strategy to try to confine programs to doing "what we want", but that is a horribly difficult and error-prone process.
I guess you are more optimistic than I about removing the parser/loader/system call gate bugs in any kind of near-term timeframe. The side-channel attacks exist, and could be problematic, but that is just a demonstration of an inherent, architectural weakness of the scheme. The real problems are likely to come from all of the rest of it.
Bottom line, for me, is that I think I am about as likely to run NaCl binaries from untrusted sources anytime soon as I am to run ActiveX controls. Maybe I am behind the times, though.