I personally think that we can do this by:

• Automating this using wrapper. This will be enabled if return object will be ID (this will be assumption that delete operations will always return ID and it will remove objects from cache.
• Giving user helper (update method) to remove this from root (queries will be updated on their own basis)
• Documenting issue (by the end of the day it's upstream bug)

ping Dara Hayes Daniel Passos Stephen Coady