You said it yourself: There are TWO tickets involved. The old one and the new one. And there are two ways to get from one ticket to the other. One would be to refund the first ticket in full and then charge you for the new (cheaper) one. That's the easier and - officially - the only way to do it. The other way would be to exchange the first ticket into the second, issue an MCO for the residual value, and then refund the MCO. This is much, much more hassle than the first way, and as per IATA rules it is supposed to be done only with tickets where at least one coupon has already been used.

I don't understand why you don't like the first procedure. It accomplishes exactly what you want. Regarding the TSC for the second ticket just ask your agent whether as a courtesy it can be reduced or even waived. After all, going the refund-and-issue-again-route is much less work than the refund-just-the-residual-value-way, so the TA might give you a dicount for the second TSC. I would.

Your argument that an agent does a "mere modification" when changing your itinerary to a higher fare does not hold water. It may have felt like that to you, but believe me: They had to issue a new ticket replacing the old one. Going up or down with the price does not make a difference. New ticket, more or less work, probably another TSC depending on the agent and on the situation. HTH...