I'm pretty sure there will be libs in various languages that allow to talk to the DOM directly (e.g. in C/C++ #include "dom.h"), under the hood they would still call out into JS but the library user wouldn't have to touch Javascript. This is how most of the C API wrappers in emscripten work (e.g. OpenGL wrapper which talks to WebGL). Calling out into JS sounds like a perf hit, but overall it works very well... as long as the JS code doesn't produce too much pressure on the garbage collector, I think this is the main problem with the current JS wrappers. But since DOM operations are slow anyway that shouldn't be a problem (it's fast enough for WebGL, so...).
I've heard that native DOM interaction (no JS middle man) is on their radar via WebIDL. They don't want people reinventing the DOM via custom canvas rendering and such so making DOM manipulation painless is a priority.