My point is that those aren't the only three options.
4. Have the browser executable perform some sort of integrity check on the settings file to detect if it's been tampered with by something that isn't the browser (which admittedly isn't robust, but it's a start and eliminates at least the more simplistic malware).
5. Implement encryption on the settings file so that it can only be read or modified if unlocked with a user-configured passphrase (such as that used for Firefox Sync).
6. Use an additional config file with the same permissions as the browser executable (i.e. requiring administrative privileges to modify) for critical security settings like whether or not unsigned extensions may be installed, thus preventing user-level malware from editing it.
7. Don't sync extensions automatically (as a Firefox user with several machines, extension autosyncing is actually more annoying than it is helpful; I'd really like to be able to selectively sync certain extensions - like Tree Style Tabs and Greasemonkey - while keeping others (like themes) local to specific machines). This solves the problem of malicious addon propagation that you mentioned, since said propagation would require user intervention.
5, 6, and 7 would be much more useful in Firefox than Pocket/Hello integration, builtin PDF readers, or any of the other cruft that's started to creep in. In fact, I'm pretty sure 6 is already possible through that enterprise configuration addon (I know firsthand that it's possible to have settings locked down to administrator-only access through that).
Regardless, my other point is that by default, if malware can manipulate Firefox' settings, it can manipulate other things that are just as bad as malicious extensions (like one's stored passwords). It's already possible to mitigate password storage risks by setting a passphrase on one's password cache, so I see little reason why #5 shouldn't be possible, too.