Unfortunately, the best way to do this will require some effort on your part. First, the SQL Native Client should go on the Deployment Server as well.
Second, go to the Deployment Server, and log into the Planner environment. Go to the System Admin menu and run the Database Data Sources application. At this point, you can use whichever source you want: Local, System, or Server Map.
For each data source that is now on SQL 2005, Select it, then hit OK (you should not need to modify it at all). After hitting OK, you will be asked if you want to modify the ODBC entry automatically, manually, or skip it. You will want to edit it manually.
Modify the ODBC to use the SQL Native Client, and fill in the rest appropriately. It shouldn't have to change much as the first part (choosing the driver) is the important part.
When you hit the final OK button, the parameters you filled in modify the file ODBCDataSource.INF. You can find this file under the Client directory of your Deployment Server's B7 share. Whenever a fat client takes a package, whether it is a full or an update package, one of the last steps will be to change the client's ODBC entries to match what is in the ODBCDataSource.INF file.
Repeat for the other SQL 2005 data sources, and you should not have to worry about this again, until the next set of data you move over. Since the data source entries on the Local, System and Server Map sides should be the same as each other, you should not have to go back and repeat your modifications.
At this point, the Deployment Server's ODBC entries should have been modified, and the file taking care of the clients on a package install has been taken care of. The only machine left is your Enterprise Server. If you don't want to repeat all your ODBC mods, this would be a good time to do the registry export, and merge them with any Windows servers running JDE services.