For what it's worth, the way the Star Fleet Universe tells it, the incident at Cestus III involved two brash, young captains who fired first and faced embarrassing questions later. But it didn't help that, by this point in time, the Gorns were 0 for 2 in terms of successful First Contacts.
The first First Contact for the Gorns was with a bird-like species known as the Paravians. It turned out that the Paravians were in fact descended from a population of Gorns that had been transplanted to their home world thousands of years earlier. (Actually, the regular SFU Gorns had been transplanted to their three "home worlds" at around the same time; no-one knows on which planet the Gorns had originally evolved prior to this.) The problem was that, not only did the Paravians not remember ever having been Gorns, the Gorn fossils they had uncovered on Paravia were interpreted in their culture as being demons or devils. Prior to First Contact, it never occurred to them that they were staring at the remains of their own ancestors. Thus, when the truth was revealed, it didn't take much for things to spiral to the point where the Paravians declared an all-out war of extermination against the Gorn "demons".
Things weren't much better with the Romulans. From the Romulan perspective, the Gorns would make for a valuable source of slave labour, once the Empire conquers their Confederation. Naturally, the Gorns take exception to this point of view - but despite holding a technological lead over the Romulans for close to a century, a fateful event at the Paravian home star system led the Gorns to hold back from settling accounts with the Romulans when they had the chance.
Four Gorn-Romulan wars and innumerable cross-border "Privateer" raids later, when a brash, young Gorn captain detected the presence of "Romulans" (or rather, Vulcans) at an unsanctioned colony on Cestus III, his response was to destroy the colony. In response, the brash, young Star Fleet captain who soon reached the scene ordered his ship to open fire - though the resulting starship duel was somewhat inconclusive. (There were no Metrons involved, as they are not a part of the SFU.) By the time the diplomats showed up to talk things out, both sides realized that the whole thing had been an unfortunate misunderstanding; the Feds agreed to stay on their side of the new Fed-Gorn border, while the Gorns paid reparations for the loss of life at Cestus III and court-martialed the brash, young Gorn captain for his use of excessive force.
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It is worth noting that, even if Europeans had been out of the picture by the time the Americas (or Australia) were encountered by anyone from Eurasia and/or Africa - as speculated upon in books like Kim Stanley Robinson's The Years of Rice and Salt - even the best of intentions would not have prevented the spread of smallpox and other devastating "Old World" diseases. Unless contact was somehow delayed to the point where Eurasian and/or African societies had developed an understanding of epidemiology, as well as a series of vaccines (or more careful medical screening procedures for those sent on outbound voyages) and the forethought to offer them in anything approaching a "neutral" manner.
Which is not to downplay the sheer malevolence unleashed by Europeans across North and South America during the age of trans-oceanic expansion. But given how differently concurrent European attempts at colonization in Asia played out by comparison - where the "germs" portion of "guns, germs, and steel" was either a non-factor, or indeed worked against those from more temperate climates - there would, alas, likely have been too many potential points of trans-Atlantic (and/or trans-Pacific) contact, plus too many trade and migration routes criss-crossing the Americas themselves, to avoid some measure of demographic collapse... regardless of the arrivals' intentions.
