I have disabled that monitor as well for the same reason: we use the Base OS MP for our Windows servers, and are not interested in the disk space of the Linux and VDI VM's. Linux team has their own monitoring.
The correct target for the override is class "VMware Virtual Machine".
If you want to stop collection of VM free space all together you'll probably have to disable rule "VMGUEST.Collect.freeMB".
From the product knowledge:This rule collects the performance metric VMGuest-disk \ freeMB for VMware virtual machines.
The amount of free space (in MB) on this virtual disk.
Disabling this rule will stop collection of the metric into Ops Mgr and it will not be visible in views and reports. However any monitor based on the same metric will continue to function.
For reporting reasons I have not disabled this rule myself.
Monday morning edit...
I see you mean you want to disable the monitor on VM's with an OpsMgr Agent only.
In our environment the "VMware VMs that run Ops Mgr Agents" group is empty, but the "Veeam Ops Mgr agents running VMwar VMs" group should be usable. If not I'd turn to smarter guys here