This is quite unfortunate. Chrome Frame is one of the least intrusive ways to get WebGL support for visitors using IE8 and IE9.
I'm using it for running games with IE10 at http://store.craftstud.io/games/ along with Three.js and it seems to work quite well.
Luckily, those IE 9 users are less of an issue if IE 11 includes WebGL as they tend to be auto-upgraded. The IE 8 users are a harder case.