The Covenant specifically excluded humanity from either joining or being subjugated, because they believed they had a religious duty to exterminate all of humanity. This is because the Covenant was run (effectively) by a species called the San 'Shyuum, and were building a civilization based on the idea that they had the wisdom and power to understand and disseminate ancient technology from a predecessor race called The Forerunners. The effective head of the Covenant (the Prophet of Truth) discovered from a surviving Forerunner AI, that the humans may have actually been descendants of the Forerunners themselves.

This isn't entirely true (the Prophet of Truth didn't really understand what he was being told) but the entire political power-structure of The Covenant would have fallen apart if the Humans were discovered to be more important religiously than the San 'Shyuum.

So, as an act of political expediency and preservation, he ordered their extermination.

I believe this video covers it?