There was a long period in linguistics research where linguists thought they could understand language best by discovering the etymologies of every word; this drove a lot of the work of recovering Proto-Indo-European. They thought that if they knew where a word came from that they would then know the absolute truth regarding the meaning of the word. Things changed at the beginning of the 20th century, and this approach is now considered pseudo-scientific; linguistics is data-based now, with meanings of words determined by their usage and context.
"Master" is a pretty neutral word, with about a dozen meanings if you check Meriam-Webster. Even if the top meaning listed were "one having authority over another" (and it's not), this is still too vague to simply declare that it's associated with slavery and needs to be avoided. There's nothing about a Git repository that's directly reminiscent of American slavery, so it's quite arbitrary to declare the word "master" inappropriate in this context. It could be quite a different story if the spelling were "massah", which would directly evoke the image of slavery.
In general, though, even for actual offensive words I think the banning approach is counter-productive. Melioration, the loss of a negative connotation, is a perfectly natural process, and by outright banning a word you prolong the process or even strengthen the negativity of it. Let negative word meanings fade out of our consciousness as the negative feelings that gave birth to them disappear.