If you have a customer who wants to do this then you are not doing the right thing by trying to figure out how to get them up and running with a configuration Adobe will not support.
We had a very hard time with MS SQL Server and it is really in LiveCycle ES with MS SQL Server 2005 that we have finally got it working well. Some recommended configurations (isolation for example) are not in SQL Server 2000. I would not suggest you continue with SQL Server 2000. If you do try it, you may find it will function, following on from that the customer may have a greater expectation that they can use it, but the risks are very significant when running a configuration that Adobe does not test and will not provide support on.
the down side of using MySQL as your database is that is is generally less well understood by IT and thus may need some training on the back up and restore aspects. But the install could be a turnkey which is pretty simple assuming you are using JBoss as the application server. performance for a non clustered install with MySQL is very good in comparison to any other database. There is also a limitation if you are using orchestrations on the number of process variables you can have.