I agree that people consider anything that appears in a web browser is a "web app", but that doesn't make it right. ActiveX, Java Applets, Silverlight, Flash, and NaCL are not "web apps." People also think "Internet" is analogous to "World Wide Web."
A "web app" is something that is built using open standards that has oversight by a standards committee that is either the W3C or WHATWG.
Feel free to peruse through WHATWG's specification for "Web Applications", or "Web Apps" for short. There is a standardized, very explicit definition of what that term means.
Is it a purely definitional argument about what constitutes a "web app"? That raises the question of what exactly "the web" is and who gets to decide, on what basis - but more importantly, who cares? Let's all adopt Native Client apps in the place of web apps and call them something else.
Is it a "standards" argument against NaCl adoption, ie. "Mr. SOCKWG says No!"?
Or is it an argument on technical merit against NaCl adoption? If so, you'll need to spell it out in more detail. Appealing to "Web = Good" is a fair enough starting point, because the Web is Good, but it's not enough here. NaCl advocates (or some of 'em) are presenting an argument about why the Web is good, and how it (or some Web' that isn't the Web - again, definitions in themselves are nothing) could be better. To simply repeat "Web = Good" in reply would be make of the Web a cargo cult - and, one can't help noticing, a cargo cult which just happens to operate very much in the interests of the shrine guardians.