How do you revoke PII from a distributed information system, like anything using a blockchain or distributed version control? You don't.
If you choose to block all EU IPs instead of implementing the most basic data security and retention policies, then it’s for the best that EU users are not able to use your compromised service.
Once you've got that sorted and you can change/remove identity information, the likes of GitHub have no issue so long as they have GDPR-compliant contracts with any business partners who can access git repos. Obviously, anyone using GitHub who decides to store all identity data forever is, generally speaking, not GitHub's problem, same as someone who noted down the names of all their friends on Facebook isn't Facebook's problem.
Misuse of git isn't a problem inherent to git.
Just because you are not making revenue doesn’t mean that you don’t have to abide by regulation. The GDPR is intended to solve a very real and present issue; if you run a side project that deals with personal data, then the fact that it makes no money doesn’t mean that your mistreatment of personal data isn’t harmful!