Ward is not a double agent. He is doing this to save Skye. Since he killed the wrong clairvoyant, he has to make things right. Even if it means infiltrating HYDRA and become a sleeper agent for SHIELD to know when, where, and how they're gonna eliminate Skye.
More on Marvel.com: http://marvel.com/news/tv/2014/4/8/22302/exclusive_brett_dalton_on_agent_wards_new_role_in_marvels_agents_of_shield.#ixzz2yVTGCtj6