They didn't get upset about this when it happened before, 10 years ago, under Clinton:
Senior managers of the Central Intelligence Agency’s Directorate of
Intelligence (DI) -- the arm of the Agency responsible for analysis -- held an unusual emergency meeting with their analysts on the afternoon of 1 July, just before the start of a long holiday weekend. The purpose of the meeting was to announce plans for a complete reorganization of the Central Intelligence Agency.
[...]By April 1994, Administration displeasure with CIA had turned into indignation. Faced with a growing number of foreign policy debacles, Clinton officials -- notably several on the staff of the White House and National Security Council -- grew increasingly furious at CIA intelligence assessments which suggested that Administration policy in North Korea, Somalia, Bosnia, China, and Russia was in trouble. Administration officials started to argue that CIA was not providing them with "the proper support." Some officials implied
that if CIA had done a better job analyzing the world, Mr. Clinton’s foreign policy would not be in trouble. [...]
In private meetings with other senior DI officials, MacEachin -- who is said to have claimed that he is acting on behalf of Director Woolsey -- laid down the real objectives of his reorganization plan:
Consolidating and institutionalizing changes already made.
..."purging the culture of the 1980s" at the CIA. ...
Assuring that CIA briefings coincide with Administration policy and cannot lead policy makers to accuse the Agency of "disloyalty." MacEachin was quoted as having actually said in a recent meeting with senior CIA officials: "Analysts must recognize that if they give a briefing which deviates too much from official policy, they may be accused by Clinton Administration officials of being disloyal."...