I could not find any reliable way to do this properly and support all the cases.
We can detect that mutation was delete using numerous strategies.
I have implemented link do do so here: https://github.com/aerogear/aerogear-js-sdk/pull/173

We can easily detect that operation is performing delete using numerous options:

• Extensions
• @delete directive
• return payload assumptions (ID)

However we have no means to delete actual object in cache due to cache api limitations.
We should revise that ticket after 3.0