You can be fairly sure that an exe will happen, based on the fact that C2 is built to be able to do that without any changes to the program itself.
Yes it would **** if Scirra doesn't have a hand in that, but rest assured someone will take up that cause.
What you really need to worry about is: how good will that be, and how much will that cost you? Long story short, time is money.
One thing to think about is the advantages of having both. A mini version of your game to run in a browser, and the "epic" version on your pc at home.
Its all about the audience. One way to bring the casual players in, another to keep them there.