GDK, GSK and GTK are now part of the same *.so library. If GtkClipboard
still worked fine just before the commit that removed it, it would have
been possible to first deprecate GtkClipboard and then removing it in
3.9x+2 (see my comment below).
Of course if GtkClipboard didn't work anymore, then it needed to be
removed. Or maybe it was possible to port GtkClipboard to the new GDK
API, but this would have been more work for the GTK developers. It all
depends if you want to provide a smooth experience to port apps.