This situation will occur when you try and remove a management pack that utilities a Run As account. You’ll get an error that the management pack is dependent on Microsoft.SystemCenter.SecureReferenceOverride and removing that can be a little bit painful.

Anyone one who has ever removed a management pack with a dependency knows the old method of exporting the management pack, removing the offending refference and importing it back again. The steps for Microsoft.SystemCenter.SecureReferenceOverride are slightly different but the principle is the same.

1. First you need to remove the Run AS account from the Run As Profile
2. Export the Microsoft.SystemCenter.SecureReferenceOverride management pack
3. Edit the management pack and remove the references as you would with any other dependency
4.  Increment the management pack version
5. Re import the management pack

Here is a nice method from Matthew Long which uses powershell and doesn’t require any XML editing.

The below is copied for my records, original posting here

1. Open a powershell session with the Operations Manager module/snappin loaded.
2. Type: $MP = Get-SCOMManagementpack -Name Microsoft.SystemCenter.SecureReferenceOverride
3. Now we can view the referenced management packs by typing $MP.References
4. From the list of items in the Key column, note down the alias of your MP you wish to delete.  If you are having trouble finding it, the Value column will list the full ID of the MP.
5. Now that we know the MP alias, we can remove it from the Secure Reference MP by typing $MP.References.Remove(“yourMPAliasGoesHere“)
6. Now we can verify the MP is valid by entering $MP.Verify()  to ensure there are no orphaned overrides, etc.
7. Finally, we can save our changes by typing: $MP.AcceptChanges()