How can I reduce chromatic aberration that shifts focus between color channels in macro photos?

You are seeing chromatic aberration — a prismatic effect which, as you nicely illustrate, reduces sharpness even in black and white photography.

A lens which has greater correction for this is called an apochromatic lens — often something like "APO" in the lens name.

Note that in lenses for telescopes and microscopes, you'll often also see achromatic lenses — these are simpler and cheaper. You may also find this designation in older camera lenses ("achromatic doublet"), but it's pretty rare to see it advertised in modern ones. Achromatic lenses (or "achromats") correct two wavelengths, rather than the three we need aligned to match human vision and color photography. For telescopes, it's usually blue and red that are brought together; Canon says that for photography it's typically blue-violet and yellow.

I don't see any claims about achromaticity in the description of the EF 50mm f/2.5 compact macro; I think it's fair to say that yes, you're pushing the lens. From reviews at Photozone.de (all with the same 8mp body, so they're comparable), CA is low but higher than some other lenses; compare your Canon 50mm f/2.5; Canon 180mm f/3.5 L; Sigma AF 150mm APO — scroll to the bottom of each page for the charts.

It is possible that the problem is exacerbated by the Life-Size converter. I assume that it's this one sold by Canon to match the lens; a few reviews of that suggest that this does contribute significantly to chromatic aberration. It's probably much better than cheap single- or double-element extenders, but if you're looking to get exceptional results at this level of macro photography, you probably want to invest in a lens that is designed for "true" 1:1 macro natively — and watch the reviews for extremely low CA before buying.