Yes. When you click the "Commence Scheduling" button, the Auto Scheduler Options will appear, and you have the choice to auto-schedule:
"All remaining empty positions in this schedule"
"All empty positions in just particular ministries..."
By choosing the second option, you will be able to schedule just one particular ministry. All ministries will still be shown on the MSP Schedule and Schedule Skeleton, but they can be auto-scheduled at different times.
Note: By choosing the "Show More Options" button, you can further define what portion of the schedule MSP should Auto Schedule (e.g. just Special Services, select Services or select Unfilled Positions.