Refusing to use non-GPL software in medicine is a great idea. Also not using ANY fossil fuels is a great idea. But just because you cannot ride your bike, everywhere, does not let one off the hook regarding environmental responsibility. You still have a moral duty to reduce your use of oil. The reasons are clear, oil enables all kinds of abuses, its not good for the environment, and finally its going to run out someday. If you cannot stop using oil, it still helps to reduce your dependence. Similarly, if you cannot realistically refuse to use non-GPL or non-FOSS medical software, one should still try to loosen the grip of proprietary medical software generally. Here is a list of things to try.
Please contact me through FredTrotter.com if you have more ideas about how to use moral compromises to move the GPL Medical Software movement forward.