You are correct. In the AdES signature world, the solution is to have a cryptographic (signed) timestamp using a newer hash algorithm that rehashes all previous commits, and to include that timestamp into a new commit. When verifying the hashes of old commits, the software would verify that those are covered by an appropriate timestamp that proves that they were created before the old hash algorithm was considered too weak.

This is very similar to the following: Instead of rehashing, i.e. replacing old hashes with new hashes, add the new hashes alongside the old ones, and sign the new hashes, together with the time mark, by a trusted authority. The old hashes and signatures then remain valid indefinitely as long as the new hashes and signatures are verified successfully.