Yup. Thats a core SOQL limitation that I don't think we can get around.
The soution is pretty ugly. Change the multipicklist to a lookup relationship (many to many) and do your aggregation on the junction object. Data model surgery. Ouch..
The advantage of this is that you will be able to see how many times each unique value is associated with a record, rather than seeing all the different combinations of values that are put together in the multi-picklist field.