I think it doesn't require organizational alignment or faith in a leader for bad acting to occur. While I agree reality is more often obvious and mundane, the NSA has demonstrably not operated in the USA's best interests. The Snowden leak proves its inefficiencies, lack of oversight, and lack of access governance. History supports your point, but it also supports counter productive actions and nefarious self and private interests by individuals and small groups within those government agencies. It only takes a few minutes searching for leaks that made it to the main stream media to show both statements are true.
While this topic is about the NSA I feel this are relevant questions:
Why do we still have a FDA given they fail so regularly to catch food and drugs that harm people?
Why do we still have a FTC given they've fail so regularly to prevent monopolistic behavior from telecoms?
Why do we still have a FBI given they fail so regularly to prevent mass shootings and domestic terror attacks?
Why do we still have a NSA given they fail so regularly at sharing information allowing foreign entities penetrating our financial and tech sectors?
Surely you recognize at some point inefficiency must give way to the question, has this been done intentionally? Especially since that is supported historically.