In this context, though, the subject is the repository, an inanimate piece of property, not any other user. In that context, I'd argue that both "owner" and "master" are descriptive and very difficult to interpret offensively unless you're going out of your way to interpret them as such.
There are subtle differences in connotation between "master" and "maintainer", too - think "king" and "steward", apologies to Tolkien - it's not like they're synonyms and a swap is just being done in-kind. I think there's actually a case to be made that "maintainer" is a better label for the role, given the existing context of a project maintainer being one who has administrative control over it (and the existing "owner" root role), but to change the label with the reasoning that "master is exclusive, so we picked up a thesaurus" isn't going to pass the sniff test for a lot of people. A slightly more tactful approach of "we decided this better describes the role as it already applies to modern team organization" would have worked just fine.