... even if it took a year with no updates, and no third party compatibility.
I doubt they could do this without offering a refund. People bought C2 because they want to make games, not to wait around for a new engine. Besides, if Scirra made this switch they would be playing perpetual catch-up to Stencyl. Really, the only difference between Stencyl and C2 would be the UI. It would also nullify their tremendous advantage in HTML5 which is a promising technology. I don't know if HTML5 will be the technology to rule all the platforms, but I don't think it is in any danger of becoming obsolete in game development. However, I can see why people are getting impatient with HTML5 - the hype was so enormous and premature.
Edit:
This highly relevant article just came to mind. TL;DR, while Scirra is rewriting everyone else will be moving ahead and that obviously isn't good for Scirra.