The existence of the Gorn can't be classified if Starfleet was gearing up for a possible war with them.
The best handwave I've heard for Kirk's line about "the creature the Metrons called a Gorn" was that he was aware that the Gorn existed, but didn't recognize this variety of Gorn as necessarily being one of them, because the ones he'd been aware of before looked different. "All Those Who Wander" established that Gorn mutate swiftly to adapt to new conditions, so it follows that they have multiple phenotypes, reconciling the different appearances they've had in "Arena," "In a Mirror, Darkly," SNW, and even the Kelvin comics and computer game if you like.
The best handwave I've heard for Kirk's line about "the creature the Metrons called a Gorn" was that he was aware that the Gorn existed, but didn't recognize this variety of Gorn as necessarily being one of them, because the ones he'd been aware of before looked different. "All Those Who Wander" established that Gorn mutate swiftly to adapt to new conditions, so it follows that they have multiple phenotypes, reconciling the different appearances they've had in "Arena," "In a Mirror, Darkly," SNW, and even the Kelvin comics and computer game if you like.