Based on the article's statement that "agency employees are privately voicing frustration at what they perceive as White House ambivalence amid the pounding the agency has taken from critics", I suspect it's the "bad press" angle rather than a realization of the (negative) consequences of their actions.

You need to consider that the analysts that are complaining here, are trained to not question the motive behind their work, or the implications. They are essentially soldiers following orders, so if they started becoming critical of the task they are doing, they wouldn't be fit to do it, and lose their job.

The problem however, is that while they are trained and behave like soldiers, they do not get the gratitude that is usually given to soldiers, because regular soldiers go to combat, and risk their lives, while these stay in the basement at Fort Meade. So their only pat on the back comes from their immediate superiors, in secret.