This is such a ridiculous argument, and Gruber chooses to lead with it. So, according to Gruber, if 10 years from now everything else on iOS got crazy faster (including Mobile Safari), but web apps on the home screen remained the same speed as they do today, then Apple still wouldn't be hampering them. How can anyone even read the rest of the article after this?
But, if we do, we find the security argument is equally frivolous when it comes to home-screen web apps. There is nothing less secure about a home screen app (which is just a glorified bookmark) than MobileSafari. MobileSafari is connected to the web, which means they're already allowing anything access to Nitro. If anything, there would be a much better argument for ONLY allowing home-screen web apps, because the user is implicitly stating they trust it more (than any random page you might be redirected to).
Beyond all this, I am willing to believe the "hey, it'll come with time" argument. But we should just say that, not bend over backwards to manifest false reasons.