For all practical purposes, the passenger cancelled the ticket. The TA is an agent of the passenger, not the airline. Are you saying that the airline is required to accommodate a passenger that boarded a flight and then cancelled their ticket?
No.
But once a passenger
was previously allowed to board try to inquire about the cancelation. And if passenger seems genuinely ignorant about the cancelation, use some human judgment about how to handle the situation, rather than just rigidly follow rules.
I can't recall at the moment where I read it, nor which retailer it was (I think it was Nordstrom) but there's a story told about this person whose feet were two different sizes. He walked into the store and was going to purchase two pairs, just so he could have a shoe of the right size on each foot. The salesperson that rang him up only charged for one pair, saying that it's not the customer's fault that they didn't have one pair that matched both his feet.