I think a few of your assumptions are wrong. Large downloads are commonplace, especially for games, and lots of people have broadband so it's not a problem. Many Steam games run in to several gigabytes, for example. As a web game, WebGL renders identically to canvas2d, so there should be no need to turn it off. If you're talking about effect fallbacks, then C2 has some options to help you set up appropriate fallbacks, and you'd need to deal with that problem in node-webkit as well anyway, so no difference there.
If the engine and the game data were split in to two downloads, I think you'd get even fewer players. A single download is simple to use: download and run. With two downloads, it's a little confusing (why not one download?), plus you need to know how to set up the runner and the game download so the runner knows how to find the game download. Some people will get that wrong, or just download the runner and wonder why it doesn't work, resulting in fewer plays for your game. (You'd be amazed how much people don't read instructions - it's a constant thing that comes up in support for Construct 2. You'll get lots of people clicking the first download they see without reading anything then sending you an email when it doesn't work immediately.)
So just distribute it as a web game, or take the file size overhead which shouldn't matter for anyone with broadband!