If history is any indication, it won't be WebGL but WebDX and we'll at least write both glsl and hlsl if not directx adapted to javascript outright.
They can alternatively just require at least opengl es 2.0 support installed through gfx driver, thus only working on desktop machines. Not that it will make their plans of phone+tablet+desktop unification easier but, hey, it might shut up whining hipster developers for at least a few years until the realization that MS intentionally underdelivers dawns on them.
I agree that GLSL shader support would be awesome, but if IE didn't support GLSL we wouldn't have to hand-write our HLSL. Chrome and Firefox for Windows already use ANGLE, which translates GLSL shaders to HLSL [1].
Unfortunately, complex renderings can produce some tough-to-debug problems when things get lost in translation. The good news is that ANGLE is still quite good, actively improving, and it allows automatic translation of GLSL to HLSL.
Hopefully they just happen to have HLSL support now because it was easy and are still working on GLSL. Otherwise it's not WebGL.