Malware can do a lot of things, but I never heard of common software being designed under the assumption that malware has taken over the PC. The software I use is designed under the assumption that the user is intelligent enough to keep the computer malware free. Only the OS or explicit security software is designed to keep me from malware, but not my text editor, office software or browser.
It is a terrible excuse for ignoring user intent.
What's next? Disallowing to change the startpage from google.com because malware can change it? Disallowing downloads because users could download malware? Going that route would essentially take away the entire software in the end. Maybe at one point Firefox is only allowed to operate from within the cloud, where employees make sure it is 100% safe?
Also others have already said that one could add admin privilege to certain settings.