Now, security is important, and it would be nice if all applications could be verified as to security. But they aren't. So while it would be good to figure out how to properly sandbox desktop HTML+JavaScript applications, I don't see as how failure in that regard should retard their adoption anymore than it retards the adoption of native applications written in C.
Mozilla has used "no IE-like privileged mode" as a marketing point in the past. There's obvious benefits, but I hope any modern browser is going to be careful about the sandbox is implemented.
Would the C version of your native desktop app download code from an online ad network? Then it is just as problematic as a web app in an unsandboxed browser. If the C implementation of your desktop app wouldn't do that, then the HTML+JavaScript implementation of the same application shouldn't either, and there is no problem.
My point is simple: IE's sandbox was broken repeatedly, creating a bad reputation and scoring marketing points for other vendors.