Right, there will be a wasm.js polyfill just like pepper.js, for browsers without native support. And once browsers have native support, that polyfill can be dropped.

The difference between PNaCl and WebAssembly is simply that WebAssembly doesn't come with a pile of API expectations established by a single browser, and that it has the blessing of multiple browser vendors. Ignoring the API, the latter could have worked with PNaCl just as well.