I think the grandparent's point is specifically against embedded scripts rather than JavaScript itself, since it can be used to make HTML less like a document, and there's also the proverbial can of worms where you automatically run Turing complete code from an unknown person.
Actually I'm thinking about complexity of implementation and security consequences. I'm not sure that JavaScript interpreters are so common and bundling V8 just kind of defeats the whole purpose... Implementing JavaScript is not an easy task, it also requires implementing plenty of APIs like DOM access, XHR, complex event system, to be any useful. And ability to evaluate a Turing-complete code poses just another level of security issues.
Whether it makes HTML less like a document is up to author to decide, IMO. Some JS snippets are pretty useful, some are not. You can use JS to implement an interactive learning system or you can use JS to spy on users.
Wasm probably is easier to implement that JavaScript. But it still carries other issues mentioned above.
I'm a big fan of WASM. And I imagine that a naive but functional implementation is easy to make. However, as the web becomes increasingly heavy over time, there will be pressure on the dominant browsers to accelerate WASM, and they might resort to the same complex tricks that modern JS interpreters must do to stay competitive.
I think anything real Web 2.0 (I'm takin' it back, it's not their word anymore) would allow for both models. Whatever is next needs to be both simpler, more generically useful, and fill the requirements of this project as well as the most progressive "web app". At this point, I am open to "starting over."