While I share your concerns about the State Dept. In this case the article states that the State Dept says this was a terror training facility and the CIA is discounting that.
. . . failed to persuade the CIA and the State Department, which continued to question their credibility.
The State Department, in particular, worked strenuously to block publication of the two White House reports, describing the Salman Pak hijack drills, Knight Ridder said.