A couple points to make:
1. Why should the TA care that its Tzedakah? They are in business to make money. As far as they are concerned (at least according to my understanding of the dialogue), this was a regular client.
2. I'm assuming the price was okayed by someone. Why? Because it was a good price or bad price? That doesn't change based off the markup. In addition, as others have said: if I go to a store and buy something at the quoted price, I don't deny the charge because I think.they made too much money, even if I find it cheaper elsewhere.
3. Suggesting that the markup should be a flat rate is ludicrous. I don't know any successful small business where that would work. A $6,000 ticket should only make the TA $100?
4. To suggest denying the charge....um....what happened to making a good faith effort at a resolution (assuming that there is really an issue)?
5. The TA probably got defensive because some random person came out of the woodwork 11 months later and accused her of overcharging. We all would get defensive at that.
6. How much does a baker markup his prices? Grocer? Restaurant? I don't care. I buy based off if I think its a normal price or not.