It works better if the group is sinister, whether they're a HYDRA offshoot, AIM lackeys or something else. A Wikileaks-lite group doesn't bring much menace and drama to the situation since all they can do is expose things SHIELD is keeping secret. The whole premise of the show is that SHIELD knows it can't keep everything secret, so they're working to protect the public and manage the riskiest people and technologies. It makes more sense in terms of the world SHIELD operates in for Skye to be the dupe of the sort of people whom the organization is fighting against. A "hackctivist" plot takes very little to resolve. Infiltration by a HYDRA operative would be far more dangerous, especially if she sold out SHIELD's activities in the belief that she was helping the public. Imagine the team taking down an extremely dangerous subject like Molecule Man, only to have Skye give her cronies that person's whereabouts and help "liberate" him. As Coulson pointed out in the pilot, some groups would want to exploit that sort of power. Someone of that potential in HYDRA's hands would be an extreme crisis, one that would force Skye to face reality and might cost the team everything.