What is proof for reimbursement now? All the receipts are laser printed anybody with a scanner can make them out to be as much or as little as they want to be. Credit card statements are available online or as a PDF, a few key strokes and poof, new rate. There isn't any way that the people verifying these charges can tell the difference, as it's just a laser printed document.
Airline tickets? You can change that to whatever you want it to be, as the price isn't on the boarding passes.
The hassle is with your reimbursement people, not with the hotel. A receipt was given at the time of purchase, and you got one saying you were in the hotel. If they require the hotel issued receipt then you obviously can't do net direct rates (or for that matter travelocity or any other prepaid arrangement).
I don't see this at all as being a hilton issue, they can not possibly provide for every situtation of the accounting departments out there.