gtk and gtk-sharp are actually unconditional depends in the ebuild. The gtk USE flag seems to pull in gnome-sharp; if this is right it should be renamed to the "gnome" USE flag, or if gtk is actually conditional then it should be in the gtk?() block.
gtk+ is an unconditional requirement of beagle.
The gtk use flag controls whether the UI gets built. gnome-sharp and co are requirements for beagle-search but not for the core beagle daemon itself.
I think the gtk use flag is more appropriate here as the beagle-search GUI is not GNOME-specific.
But it pulls in a whole load of gnome packages, including gnome-desktop, gnome-panel. Compare:
USE="-gtk -gnome" emerge app-misc/beagle -vpe|grep gnome
USE="gtk -gnome" emerge app-misc/beagle -vpe|grep gnome
4 packages versus 23 packages.. the gtk use flag is pulling in 19 gnome specific packages.
Use flags are about functionality and not the dependencies which they bring in. This flag adds a GTK+ GUI, *not* a GNOME app.
This bug was already reported previously and Daniel is right we can't do nothing about it.
Hmmm well the beagle FAQ disagrees with you:
"The included user interface is a GNOME application, but it too is an optional build. There are many other search interfaces that are shipped separately. KDE interfaces include Kerry and yaBi" - http://beagle-project.org/FAQ