So what kind of covenants do you think will be in the game? Other than Darkwraiths because it wouldn't be Dark Souls without them now would it? So let me go on a little check here...
Gravelord Servant: Well Nito's dead so either they are replaced or there is some kind of remnants of them (like some lich that you talk to and then you join them.)
Forest Hunters: Well, I don't really think we will be going to the forest (or ruins of Oolacile) so they will probably be replaced.
Darkmoon Blades: Gwyndolin's dead so I don't see them just walking around killing Darkwraiths and such, so probably replaced.
Princess Guard: With Anor Londo fallen to darkness they are pretty much dead... so they will be replaced
Dragon Covenant: With the return of the dragons they might have much to do with the story.
Way Of White: As long as there is clerics around they will be around here...
Chaos Servant: The Fair Lady is probably dead by now... so replaced.
Warriors Of Sunlight/Sunbros: Well, either Solaire survived, there is a fellow Sunbro who you talk to or they get replaced too.