Kirk,
Media Pro uses a "Light Table" for comparing images (up to 6). Invoked by a keyboard shortcut or menu, Light Table may be displayed as either a full screen UI or floating window (samples below). Independent zooming is done by unlocking Scroll Lock ('S' key) and either hovering over the focus image and hitting +/-, or control clicking on the focus image to use the contextual menu and Set Scaling submenu. The Scroll Lock item is probably misnamed; it should have been called "Scroll/Zoom Lock" since that is how it behaves. (Oh, and I always use full screen view, never the floating window, since I want to maximize screen space and not be distracted by the background UI.)
I imagine something similar could be done in the existing PM preview UI but it would require some redesign of the Zoom section's controls. Consider a single Scroll/Zoom lock checkbox and relocating the Zoom ratio control to a contextual menu for each image.