Free speech as a concept isn't just about the first amendment and isn't just about the law. Free speech can be defended on any number of grounds, and many of them apply equally to privately enforced speech restrictions. For example, consider John Stuart Mill, one of the founding figures of modern liberal thought. In On Liberty, his spirited defense of free speech, he argued that shunning or widespread ostracism for expression of particular views was a danger, and would ultimately harm a society that engaged in it, even if the views being suppressed were obviously wrong.
"Free speech is only first amendment" is a shallow and ignorant view of the intellectual tradition of free expression.
What privately-owned properties do you know of where the owner allows guests or customers to speak as freely as if they were on the sidewalk, without fear of recrimination from the owner in the form of censorship or ejection? I can think of 4chan, maybe some IRC channels.
Mill also said that the Harm principal trumps freedom of speech (i.e. individuals should be prevented from causing harm to others and/or property at the cost of their liberty).
He also says that the offense principal should not trump freedom of speech, but acknowledges that there are cases of offense that cause psychological and social harm that still qualify for the harm principal.
Was the repo code change harmful? Maybe, depending on the definition of property. Mill saw freedom of speech as a path to the truth, and he also understood that principals and rules change over time. I think he might be in favor of Github censoring their repo since it was their property and not a crucial debate towards finding the truth.
"Free speech is only first amendment" is a shallow and ignorant view of the intellectual tradition of free expression.