Practicality matters. For example, even if you choose not to harm other living things, you cannot avoid stepping on and killing the occasional insect. Theoretically you might be able to do it, but you’ll stop having a life. But you can still do much in line with your beliefs, such as not killing animals for food.

If GitHub were the sole game in town, maybe (probably) they wouldn’t have switched. But it isn’t, and they found something which in their view is an acceptable replacement and less worse. So yeah, maybe they don’t ethically agree with everyone on every thing up the chain, but they apparently agree with them more. That matters. You take a stand where you are able to.