Hi Greg -- the only good option you have left is to run in full-screen mode. In full-screen mode, there is a icon on the toolbar with display options. Click it and select "Swap Displays".
(There is a bad option: if you start Aperture with the menu bar on the external display, and set the Secondary monitor to "alternate", and then move the menu bar to the main display using the "Arrangement" tab of the OS X Display Properties, the menu bar will end up on your iMac but the Aperture displays will be reversed: Aperture's Primary display will remain on your external monitor and the Secondary Monitor display will appear on your iMac. This is frugly, imho -- that's fragile and ugly, not likely to last, not worth learning, and not suitable for real work.)
Fwiw, I tried the good option for a while for similar reasons, but I settled on moving the menu-bar to the external monitor. This is automatic -- when an external monitor is not attached, the menu bar (or course) returns to the only display. In my case, though, my external monitors are much larger than my main display (which is 13").