Thank you for the post.
The guide suggests to use the original installer to uninstall; however, if that's not working, then stop the FileMaker processes in Activity Monitor, trash the entire FileMaker Server folder located at /Library/FileMaker Server and restart the computer. That should uninstall the program. Please make sure to first back up any databases, schedules, and groups as trashing the entire folder will remove these.
For more information on the location of the databases, backups, schedules, and groups see page 56 of the FileMaker Server 12 Getting Started Guide.