The way I have dealt with this is upon check-in to the hotel (and when they didn't listen once or twice, on checkout,) when I asked them to put both rooms on the same folio, and bill it to my room (it worked out as you say - I received one stay credit, one day credit per day, as if I had booked one room - but received the points based on the entire folio.)

This has worked when we have travelled with another couple, for instance. And I still have had to contact HHonors about these issues on occasion, but they have been helpful so far. But both reservations have been made in my name in all of these, iirc.