Your analogy to mythology is a very good one, and it certainly makes one think. To look at another analogy - the meteor that ended the reign of the dinasaurs cleared the way for mammals to develop into us. Who's to say that the dinasaurs wouldn't have evolved into at least one satient species on their own if it weren't for the meteor. From our perspective, the meteor was a very good thing, but it made our existence possible by destroying what was before.
Now in the case of the W'rcacnter, as creatures of chaos, they are completely incompatible with the universe as we know it. Now chaos is usually not a good thing, but prehaps that chaos would ultimately clear the way for something else to come along that is equally intelligent, aesthetic and relavent as we are. The problem is, how many of us would be willing to sacrifice ourselves and the only reality we know of on the off chance that the W'rcacnter will pave the way for something better? Our marine is definitely not a W'rcacnter - the is nothing about him that comes close to fitting their description - and he has no choice but to try everything possible to prevent the W'rcacnter's release.