Humanity only stands out because the Covenant were trying to exterminate them, not assimilate them. That’s a massive difference and the real distinction.
The only comparable conflict we know about re: the Covenant would be before it’s formation, and the war between the Prophets and the Elites. It was apparently long and bloody and started out with the 2 sides trying to wipe the other out, but with the Elites proving so formidable, once the Prophets consistently had the upper hand thanks to the Dreadnaught alone, they shifted tactics and “partnered” with them.
It’s a very different situation. In every event, the Covenant either intimidated the race into subjugation or fought a war to do so. The Covenant was not trying to wipe them out.
Yes, because it was a dire conflict, but the Covenant still wasn’t looking to eradicate them unless they absolutely had to. The Arbiter glassed part of the Balio to break the Grunt’s resolve and then the Grunts were not only absorbed back into the Covenant proper, but were elevated from simple labourers to being able to gain position and status in the military as well.
Not that the Grunts ever had it good, mind you, but it’s still quite the step up from extinction.