I had the same problem, I think the problem stems from when you choose to downgrade to 4.1 (sudo apt-get install mysql-server-4.1 or through synaptic) it selects to remove 5.0 server, but not COMPLETELY remove 5.0, which is where the conflict lies. So if you manually remove 5.0 server first, debconf will prompt and ask you to remove all prior databases. If you remove all databases this way, 4.1 installs without a problem. (I tried this on my Ubuntu Dapper Drake 6.06 LTS install)
Being new to apt, I don't know if it's possible to modify the dependencies this way. Maybe just changing the error message so it says, "incompatible databases" instead of dkpg failed during subprocess 1 (--unpack) -- downgrading mysql-server from 5.0 to 4.1 fails on install https://launchpad.net/bugs/36868 -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
