It could be that the "neutral goblins" thing is a programming shortcut. I'd assume that the programmers set it up so that killing any human NPC (unrelated to the quests, of course) would result in a reputation loss. In terms of simplicity, it is easier to classify Marchon & Co as something else rather than code in no rep loss for killing just those specific humans.
The reason I think you don't lose rep is that no neutral or good NPCs know they're there. Hence, your party can keep it secret.
I've killed them off a couple times, but it just doesn't feel right.
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