Both Jonathan and Charles are right... you've got to stop the service first, then uninstall/reinstall. Combining their two answers makes the perfect batch file or PowerShell script.
I will make mention of a caution learned the hard way -- Windows 2000 Server (possibly the client OS as well) will require a reboot before the reinstall no matter what. There must be a registry key that is not fully cleared until the box is rebooted. Windows Server 2003, Windows XP and later OS versions do not suffer that pain.