git as-is is completely unfit for purpose and a huge security risk for this use case, because it uses MD5, which is no longer collision-resistant.

If your proposal is 'something like git, with a few modifications to make it suitable for this use case', then that's exactly what I'm proposing. What you will need, once you've considered all requirements to the best extent feasible, will be a blockchain. Eg you do need the ability to make protocol updates, no matter the time scale of transactions.