According to the upstream page (http://live.gnome.org/Empathy/Install), libpanelapplet is *optional*; there is a compile-time switch provided if you want to build the megaphone & nothere applets.
The source code seems to confirm this; see configure.ac.
There needs to be a USE flag of some kind in the ebuild for this, that way those of us with non-Gnome desktops can install Empathy without dragging along a boatload of Gnome deps. For example, it'd be easier to transition away from Pidgin to something friendlier, like Empathy, if only it didn't bring Gnome to the party.
Added 'applet' USE flag 2.24.0-r1. Thanks for the report :)