I don't know the written rule but the pitch count is clearly there for pitcher arm safety so logic tells me if he didn't throw a pitch, why count it? (If there were two pitches actually thrown, those should count) So, I'm with TD at least to the extent that pitches not thrown shouldn't count, unless the tourney rules clearly spell out otherwise. TD is supposed to have the overriding say-so anyway when a rule is not clearly spelled out, as he did. That said, if the TD was actually aware that two pitches were thrown, but still wants zero pitches charged, that doesn't make any sense either.
Also, if i'm coaching summer travel, I want my players to have the attitude of seeking the most competitive opportunities. So, if that is one of their better arms, hell, I want him to throw more and hope my players would want that too. Or, at least not care who's throwing.