Optically there is very little difference between the 100mm macro USM and non-USM. The bigeest difference is that the USM version does not get physically longer when focusing closer. The non-USM version of the 100mm macro gets nearly twice as long physically when focused at 1:1 than when focused at infinity. The non-USM version gets physically longer the closer you focus the lens.
This is a decided disadvantage when trying to light your subject with natural light and/or flash. You can use a ringlite with both lenses but a ringlite delivers flat and unattractive lighting.
Also, since working distance is measured by Canon, from the film/sensor plane, the USM macro will allow for a greater working distance from the front of the lens to the subject being photographed. The USM version of the 100mm macro lens has decided advantages over the non-USM and is well worth the price difference between a used 100mm non-USM lens and the current 100mm USM macro lens.