NaCl, on the whole, is sound. There have only been a few attacks against it, and those were largely during the "come own us" phase. I'm sure there will be further attacks against it, but that is the last issue in play here. Cross-platform and existing standards compatibility are by far the more important ones, not to mention the benefits of code you can optimize as you see fit (Javascript, Flash, and other high-level languages).
Worrying about sandbox escapes from NaCl is silly when you consider the insane attack surface that existing browsers expose to the JS engine.