It's not hard to fix this problem without hurting morale. Change the primary thing that they should have morale about from protecting the security of the nation

It's not hard to fix this problem without hurting morale. Change the primary thing that they should have morale about from protecting the security of the nation to protecting the values upon which this nation was founded, namely the Constitution and the Bill of Rights. Every single agent should know the Constitution back to front, inside and out, and see it as their job to protect it over all other objectives, including catching criminals (imho, we should substitute criminal for terrorist, whenever that person is within the borders of the United States and subject to its laws.). The atmosphere at the agency should be such that any subversion of the Constitution by colleagues and superiors should hurt morale among agency employees. If you catch a criminal, but do so by subverting the Constitution, you should feel shame, not pride. When you have the power the agency has, it is of utmost importance that values be palpable in the air among staff. Power without obligation to something higher like the Constitution and Bill of Rights will always be debased in favor of achieving concrete objectives. If we're worrying about hurting their feelings, we're having the wrong debate.