Stopping SQL Services on Active Node
When configured as a Cluster in Windows, you need to control the SQL Server Services from the Failover Manager, not SQL Server Configuration Manager. In Windows Failover Manager, you can fail the resources/services to a particular node and then carry on with your needed activity.

The database engine and SQL Agent are cluster aware by default. Other SQL Server services (SSRS, SSAS) can be added as cluster aware resources, but their default behavior is not cluster aware. As far as I know, SSIS is still the only service that cannot be made cluster aware (i.e. it has to be installed on all nodes and started/stopped with SSCM on each node).

We accidently stopped the SQL Agent from the Configuration Manager, and it showed Partially Online as you mentioned.  For the cluster to get happy again, we had to offline the Agent from Cluster Manager, and then bring it back online from the same place.  The point to be made: always control failover or instant restarts or offlines from the FCM.