You don't XSetInputFocus (which is a hack) but rather fix the WM_HINTS, which is the real issue here (and not the window manager). If you want examples please search my posts, qwerty's patch to xev, or the multiple debian bug reports opened about the issue (in apps/toolkits).
Is it not possible to write a tiny utility that will set the WM_HINTS on any arbitrary window? I could use wmctrl to find the window ID of the broken window, and then use this little fixer utility to fix the WM_HINTS on that window... That would be a very very workable solution for me.