I would consider that the worst scenario. If each website was its own binary application it would undo the open source aspect of websites (even though that's only partly true today due to all the obscured javascript). But maybe that would actually be desirable for all companies which rely on advertising revenue and want to prevent any modification of their web content (such as removal of ads). It'll be interesting to see how the web develops in the future. WebAssembly definitely seems to give more control to the author.

If you are using the XHTML syntax, you could send it in a binary XML format such as Efficient XML Interchange (EXI). (Never seen anyone actually do this of course, since browsers don't support it; not sure if it is a good idea either - would it really be much faster than just say GZIP, sufficiently so to justify the extra complexity?)