Well, the HHonors T&Cs state:

"The term "eligible folio charges" for Hampton Inn®, Hampton Inn & Suites® and Homewood Suites by Hilton® hotels mean room rate only."

I would think you could argue that you paid a room rate and should get points for the entire room rate - I'd consider escalating to HHonors or Guest Assistance...

What's next, stripping breakfast or dinner out of eligible package rates?