You're correct, disabling (or un-assigning) a package should disable all alerts that are contained inside that package. In this cause it should cease Performance Monitoring alerts that are related to SQL Server.
The first troubleshooting step would be to make sure the remote hosts have the latest configuration revision. Please click the computer icon on the very top of the tree and not the orange bar appearing on the right, main pane. On the top right of that pane you will see "Configuration Revision" along with a revision number. Please note that number down.
Then, select the group from which you are receiving performance alerts and click the "Check Status" button in the ribbon and "Go". Does number in the "Config Revision" column on the right side match the number you noted down earlier? If it doesn't then you could try to push the configuration again, and possibly restart the "EventSentry" service to force a configuration update.
Please let us know if that helps.