i'm going to say maybe, i mean the covenant now allie the humans(thanks to the elites), so i am going to say probably.
The Covenant broke apart. The prophets were all killed, the brutes scattered, and the elites went to hunt them down. The elites also left the humans because if they stayed war between them and the humans would be inevitable. The grunts and jackals returned to their home planets. So, no, they probably won't be in Halo 4.