My bet is no, as in the end of Halo 3, the Covenant's leadership is gone for the most part, and everyone would be scrambling for power. It is possible that the races may be separated into their own species, but I'm no expert.
Remember, the Covenant was fragmented during the Civil War. However, Loyalist remnants still roam the Orion Arm, looking to fight the Humans and Seperatists wherever possible. These Loyalists are not organized and have no leadership, thus posing little to no threat to Earth. Actually, the greatest threat to Humanity are the Sangheili (Elites). The Elites are master tacticians and fighters, and are much more lethal than the Loyalists. Besides, the alliance between the UNSC and Elites was shaky already, and with no more reason to ally, they most likely are not such any longer. If there would be any Covenant in Halo 4, it would have to be the Elites, though.