I believe that branding should be present whenever the GNOME Panel is present, but it shouldn't be welded to "Applications" on the Main Menu applet. Branding is just that important for a default GNOME setup.
The thing with the Panel is, applets should work in harmony. We should consider the behavior, positioning, appearance, etc. of other applets when touching one applet. The distro icon should be removed from "Applications," but it should be moved somewhere else (in another position in the applet or on another applet). That's just if the Main Menu is being used. If something like the SLAB menu replaces it, it's a whole new story.
Regards,
Allan