I may be wrong as I'm not using much python (except for portage and my session manager) but unless I misunderstood all of the Changelog entries, as of pygtk 2.6 all of OpenGL stuff was removed from pygtk, so the dependencies of opengl useflag are not used in any way.
indeed, it seems pygtk splitted its opengl bindings into pygtkglext. Afaics, the tree is ok with that so I'll just remove the USE flag and dependencies on pygtk-2.12.1
fixed in CVS