While it won't give you the points, you could make an issue out of it with the restaurant. You could talk with or write a letter to the manager of the restaurant, especially if it is someplace where you dine frequently. Explain the situation and how the waitress changing what she charged you, albeit less, actually hurt you (not recieving 5000miles).

Not to mention the fact that she changed what was on the reciept. If the waiter or waitress can so easily and willingly change what YOU wrote on the reciept, how do you know this isn't common practice for them. And if they can down charge you, they could be up charging someone else. Definitely talk to the manager or owner.