There have been times when the CIA didn’t trust the president. JFK, Nixon, and Carter for example. But those differences concerned policy, not the keeping of secrets. With Trump, the agency doesn’t trust him to protect the identify of their spies. So they pulled a spy out of Russia, rather than risk his life.
The decision to carry out the extraction occurred soon after a May 2017 meeting in the Oval Office in which Trump discussed highly classified intelligence with Russian Foreign Minister Sergey Lavrov and then-Russian Ambassador to the US Sergey Kislyak. The intelligence, concerning ISIS in Syria, had been provided by Israel.
The CIA’s mistrust is well-founded, based on one of the most startling stories of the Trump presidency. The CIA’s concerns
continued to grow in the period after Trump’s Oval Office meeting with Kislyak and Lavrov. Weeks after the decision to extract the spy, in July 2017, Trump met privately with Russian President Vladimir Putin at the G20 summit in Hamburg and took the unusual step of confiscating the interpreter’s notes. Afterward, intelligence officials again expressed concern that the President may have improperly discussed classified intelligence with Russia, according to an intelligence source with knowledge of the intelligence community’s response to the Trump-Putin meeting.
The CIA’s comment does not amount to a denial.