It's possible that a compromise might be the "Secure Cookie" equivalent of specifying policy (HTTPS-only) when creating or importing keys, but I hope it doesn't come to that.
That said, I'm also a big proponent of requiring some sort of sane CSP settings to also narrow the scope of the API usage ( http://www.w3.org/2012/webcrypto/track/issues/21 ), but that remains an open issue.
For what it's worth, at Dahl's suggestion (and because I was off work sick yesterday), I read every thread on the mailing list archive and saw the design issues that were batted around on this. I now think the overall goal of this effort is unfortunate and the effort is star-crossed.
I have more respect for Eric Rescorla than anyone else I can think of working in standards, but interoperability with existing crypto is a terrible, terrible goal for a web crypto API. I'm not saying "no good can come of it", just that I can't think of any good that is likely to come of it and I can think of a lot of bad stuff.