We've been doing this on the desktop for years.
I'd like to pose a question to the authors:
Don't all the premises you've based "Javascript Cryptography Considered Harmful" on apply equally to downloaded desktop software?
-A chicken egg problem
-A malleable runtime for apps with admin access
-Code verification being defeated by other hostile apps on the system
-Inability to trust the secure keystore because of the chicken-egg problem and other hostile apps installed prior to the crypto app's installation.
-The weakness of pseudo-randomness