While our audit demonstrates that this scheme shouldn't be expected to be cracked without a critical vulnerability making its way into your browser, it does introduce some odd dependency relationships that certainly introduce new attack vectors not seen in the TOFU property of regular standalone apps.
For example, given that the NSA can be assumed to be indiscriminately passively logging all HTTPS traffic, imagine that one day they gain the capability to break 4096-bit RSA: in a targeted attack scenario, suddenly they can now go back through their traffic logs, find whichever public key is pinned in a particular Cyph user's browser, compute the associated private key, and undo method #2 as descried in the linked reddit comment (the "permanent offline" trick), which gets them half of the way toward completely breaking that user's TOFU.
That having been said, I consider it a perfectly acceptable and pretty neat solution to the problem. Is there something else you're seeing that makes you object to it?
Edit: If your objection isn't to WebSign but to the Web / JS as an execution environment in general, I'll throw in a link to this note on how we're mitigating those traditional risks while also benefitting from the sophisticated sandboxing of modern browsers: https://www.reddit.com/r/encryption/comments/4027ci/how_2_sp...