It's trivial to install a keylogger.Which is why Linux desktops really need a secure attention sequence such as the Ctrl-Alt-Delete used by Windows (and before that, VMS). No application may trap that keystroke, and it leads you to a screen with only the password entry dialogue and (as far as I know) no communication with other parts of the desktop.
It's kind of embarassing that for many years Windows has had better security than Linux in this one area. The 'schoolboy attack' of locking the screen and bringing up a fake password dialogue is also trivial.
So I quite agree that conditioning users to type in their password (or, perhaps worse, the root password) all the time is a terribly bad idea. However, asking them to hit Ctrl-Alt-Delete and enter their password into a secure authentication screen will piss them off, and perhaps also condition them to ignore the boring message and just authorize the action every time, but at least it does not have the problem of keyloggers or trojan websites which pop up 'enter your password' dialogues.
Non-technical users, who (demonstrably) cannot distinguish between genuine password prompts and bogus ones from malware, can at least be told to always hit Ctrl-Alt-Del before entering their password. It may not be enough, but at least it's something.
(For remote access, a remote secure attention sequence is also possible; for example many Windows remote desktop clients have a 'send Ctrl-Alt-Del' menu option, which again cannot be intercepted by ordinary applications.)
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