So, you're expecting a Deus Ex Machina solution to SHIELD's Civil War. Got it.
Of course, the problem is that 5 out of 6 heads of HYDRA have been dealt with so far, the 6th, Dr. List, will be very soon and Von Strucker will be taken out of comission in Avengers: Age of Ultron. Who do you expect to order such an attack? HYDRA's motto of "cut one head, two more shall take its place" is meant to symbolize the organization's ability to never fully die, always being able to rise again by reinventing itself, not that they're able to replace heads in a very short notice. Pretty sure Marvel's intention is to have HYDRA be a non-issue for the time being, until they decide to bring it back under new leadership (Baron Zemo in Civil War, perhaps?).