I don't think the navigation box in zoom mode can be moved. Neither the help text nor the Aperture user manual indicate, that this box can be moved elsewhere. So, if the navigation box get in the way, pan the image a bit. Hold down the Space bar and drag the image away from the navigation box.
Thanks for your response, Leonie - that's exactly what I've been doing, and it's a pain in the neck, especially as the kind of fiddly little edit that requires work at 100% (removing phone lines etc) is often on the edge of the image anyway! I was hoping there was a real solution. Apple, are you listening??