Unfortunately, integrating a new runtime like <script type="text/lua" src="main.lua" module="lua.wasm"/> will probably never happen. A link tag, to me, specifies a static resource rather than executable code (although since CSS supports animations now that's probably a distinction without a difference.) <object> might be a good candidate but I don't know if it's still supported.
But, we can't get rid of JS altogether. Browsers will have to support javascript indefinitely, otherwise most of the web becomes unreadable. That being the case, using JS to load WebAssembly seems like the most reasonable backwards-compatible compromise available.
What? The original WebAssembly announcement[1], which can be viewed as the manifesto for how WASM was envisioned, it clearly says "once browsers support the WebAssembly syntax natively, JS and wasm can diverge". Eich's goal with WebAssembly is not replacing JS, it's providing a better compilation target for other languages. WebAssembly is a replacement for asm.js, not JavaScript. No one is selling a lie here.
[1]: https://brendaneich.com/2015/06/from-asm-js-to-webassembly/
That certainly is a shame, but it's not like we have to accept that as the future. HTML is a document markup language, but we've hijacked it to build interactive UIs. It might be that WASM is just a native-ish FFI system for javascript today, but tomorrow it could be something completely different.
WASM can be great if they allow it to.