You can't remove the integrated MySQL database in OS X Server 10.6, and the add-on database is encountering a conflict on a system-wide construct. You can migrate the contents of the add-on database into the system database, or can shut down the parts of the add-on that are conflicting with the system database — likely the sockets. You can also shut down the system-defined MySQL, if there are no other OS X Server services using it. Alternatively, consider an upgrade to OS X Server 10.7 or later, which replaces MySQL with PostgreSQL, and thus removes the immediate conflict.
In short: no, there isn't a way to "gently" point the system-installed references somewhere else. You might get lucky with shutting it down and allowing tools that use the sockets and related to silently reference the new database, but there'll still be some references around to the system-defined locations. These cases tend to get tangled.