First Deadly Encounter has put up an item on the Halo Wars announcement; there's one particularly interesting tidbit there that places the game at the beginning of the human-Covenant conflict:

"Halo Wars" places the player in command of human UNSC armies as they deploy for mankind's first deadly encounter with the enemy Covenant forces.

Given that the novels tell us the Spartan program did predate this conflict, it certainly doesn't preclude them from being in the game-- and the trailer does show them.