But not everyone wants to give money to apple to be able to deploy their apps, so the "sensible" way is to use hacks[1] to have a normal html5 behavior.
If you give web developers any way to disable zoom they will disable zoom whether it's appropriate or not. With an app that gets human reviewed you can make rules like "this feature can only be used for full-screen games" but not on the web where there's one set of rules for everyone.
There are actual accessibility reasons for wanting to take control of pinch zoom behavior. As long as I'm actually catering to accessibility, if I have to be forced to use the OS pinch zoom to do that it's going to be LESS accessible. The OS pinch zoom only works for text and static 2D images and nothing else. If you try to OS-pinch-zoom a 3D object on a web page, it zooms the whole UI and not the object. That's a major accessibility problem for say a website that offers 3D models.
And no, I don't think "create an app" is the answer as another comment said. I want LESS apps, LESS spyware, and more in-browser, fully-featured, perfect mobile experiences designed in HTML5 because it's MUCH harder to invade privacy with HTML5 than it is with a native app, and if Apple would stop compromising HTML5 features, a huge number of mobile apps can be implemented in it.
Why doesn't it zoom the object along with the rest of the page?