The problem is that it's essentially just another dialog or control to be scripted or socially engineered around. You can make it more onerous because it's basically a one-time action that's not something most users will do, but to what degree is adding a signing key before install different that a dialog asking you if you really want to install this third party extension?

Until you have different access levels and can both restrict users/programs from running at the base level required to do this, and condition users to recognize when increased access is being requested, I don't see this problem going away. Windows UAC is basically what we're talking about, and it still took years to users to understand it and not just always allow it (if that's even true!), and that's a system shared over all of windows.

I think the only sane way to accomplish this that worked for users and didn't cause enterprise admins to totally shun Firefox would be to piggy back on Windows' certificate store and register certificate for Firefox use only (I assume this is possible, I'm pretty sure you can do this for app-to-app communication such as MSSQL encrypted connections), but then you have to make sure you also handle the mechanisms to do the same in Linux and OS X, and now we're seeing it's a much more complex undertaking.

Protecting users from their own stupidity is a tough and mostly unsolved problem. Punting and eating their own resources to provide the safest solution they can, even if it's annoying for a more technically literate subset of users, is a solution I can understand and respect, even if it's problematic for me, because it's putting safety and security the majority of users over a simple solution that would be worse overall.