Probably not to GitHub or the courts. If in a few years it is discovered that GitHub missed something they can tell the courts "We did our best to comply, look at all the accounts we killed [and other evidence], so go easy on us for an honest mistake." In general the courts look kindly on someone who tried their best to obey the spirit of the law but missing one hidden detail.

If you are affected you could take this to court, and might even be able to convince them that the law went too far in incentivizing GitHub to delete your account. It seems very unlikely, but with a good lawyer courts can do weird things. If you do pull this off, then that would change court precedent, and when combined with a few dozen other cases eventually make it so courts will not accept deleting all accounts as a useful to to prove attempting to comply with the law. (Let me be clear, I doubt you could win this case, but it is theoretically possible so I offer it for completeness sake)