But your confidence in GitHub's continued existence comes from its network
effects, no? And competing services can only gain such network effects if
more people use them. So to me this feels like a defeatist argument.
Of course you can't put a million users today in a service used by a thousand yesterday, but I don't buy the "non-profits don't scale" argument. If that were true, we wouldn't have Wikipedia either.
I only take an issue with "I think MS is morally reprehensible but everybody uses it so I'll keep using it too" because it's a self-fulfilling prophecy. Most people looking for code hosting will use whatever they first run into, so when you choose a host for your project you are also directly channeling users towards said host. It's your responsibility to pick a host for your projects that isn't evil by your standards, whatever those may be.