You don't actually have to go that far; there are plenty of Chrome settings controlled by command-line options, and that's usually safe enough—it's actually really hard for malware to "sneak in" command-line options (if the user is a regular user, while the the Chrome shortcuts in the Start Menu et al were installed under elevation, which is the usual case.) There's a command-line option to Chrome that entirely disables the sandboxing protections, for instance.
My distinction was just that there's absolutely no way to have a UI-based mechanism for disabling nags, since behind any UI is a persisted flag. If you're up for editing your shortcuts to add command-line options, that's fine.
You mean shortcuts placed in the All Users Desktop/QuickLaunch/StartMenu folders? (I'm guessing it's just "hiding" them with a Desktop.ini entry, rather than truly deleting them?)
That's probably fine, actually, as long as the user (i.e. malware) isn't allowed to create their own shortcuts to replace the deleted ones. I assume there's a GPO to disable the per-user Desktop/QuickLaunch/StartMenu folders, so that only the results from the All Users ones show up?
My distinction was just that there's absolutely no way to have a UI-based mechanism for disabling nags, since behind any UI is a persisted flag. If you're up for editing your shortcuts to add command-line options, that's fine.