Deleting a Mobile Connect instance of a contact only (without deleting the entire contact)

Can't say if this will work, but when looking at getDeleteOptions there are two parameters called ListType and ApplicationContext. On the latter, there is the ApplicationID that can be provided.

Looking at the response there is the adapterKey with value ContactDeleteProcessor.MobileConnect that you'll probably need to target.

Eliot has posted an example calling both ContactDeleteProcessor.ContactBuilder.Roots and ContactDeleteProcessor.MobileConnect adapters together in the API call, so I would give a try (on some test Contact) by only targeting the adapter for MobileConnect through the adapterID attribute and see if that works.