The subscription engine can't compare values from two different relationships, but, I do have a workflow assembly that can be copied to the workflow server to handle this. You just need to export your Management Pack that defines your workflow and add a
new workflow array parameter of "UserAliasOrRelationshipsToSkip", plus change the assembly name and type like this:
<WriteActions>
<WriteAction ID="WA" TypeID="SystemCenter!Microsoft.EnterpriseManagement.SystemCenter.Subscription.WindowsWorkflowTaskWriteAction">
<Subscription>
<VisibleWorkflowStatusUi>true</VisibleWorkflowStatusUi>
<EnableBatchProcessing>true</EnableBatchProcessing>
<WindowsWorkflowConfiguration>
<AssemblyName>SCSMNZ.NET.Workflows</AssemblyName>
<WorkflowTypeName>SCSMNZ.NET.Workflows.WorkItemNotification</WorkflowTypeName>
<WorkflowParameters>
<WorkflowArrayParameter Name="InstanceIds" Type="guid">
<Item>$Data/BaseManagedEntityId$</Item>
</WorkflowArrayParameter>
<WorkflowParameter Name="InstanceTemplate" Type="guid">f9a5041d-1785-729d-3535-238022ad744d</WorkflowParameter>
<WorkflowParameter Name="NotificationRulesEnabled" Type="boolean">True</WorkflowParameter>
<WorkflowArrayParameter Name="NotificationTemplates" Type="guid">
<Item>2a52fd91-c6e2-a23d-f4a1-f78876c4584f</Item>
</WorkflowArrayParameter>
<WorkflowArrayParameter Name="UserAliasOrRelationships" Type="string">
<Item>15e577a3-6bf9-6713-4eac-ba5a5b7c4722</Item>
</WorkflowArrayParameter>
<WorkflowArrayParameter Name="UserAliasOrRelationshipsToSkip" Type="string">
<Item>f7d9b385-a84d-3884-7cde-e2c926d931a5</Item>
</WorkflowArrayParameter>
</WorkflowParameters>
<RetryExceptions />
<RetryDelaySeconds>60</RetryDelaySeconds>
<MaximumRunningTimeSeconds>7200</MaximumRunningTimeSeconds>
</WindowsWorkflowConfiguration>
</Subscription>
</WriteAction>
</WriteActions>
If the target user for relationship UserAliasOrRelationships is the same as that for UserAliasOrRelationshipsToSkip, no notification will be sent.
Let me know if this is of interest to you. You cannot edit the workflow in the GUI after this. Well, you can, but you'll need to add the extra parameter in and change the assembly details