Yes of course, but only during the early stages. The post-MVP roadmap for WebAssembly specifies DOM & Web API integration (http://webassembly.org/docs/gc/), so that specific case will too disappear with time.
edit: I'd like to clarify that I'm not saying wasm will boom in usage over night, but as time goes on, the rough edges clears up & features like these are added it might become the better choice.
If you read point 3 on this page (http://webassembly.org/docs/high-level-goals/) you should realize that the need for JavaScript won't be required at that point.
edit: I'd like to clarify that I'm not saying wasm will boom in usage over night, but as time goes on, the rough edges clears up & features like these are added it might become the better choice.