President Donald Trump is not the first president who has had trouble with the Deep State.  Harry Truman had a major problem, too, which revolved around the resistance by the State Department and Central Intelligence Agency (CIA) to his decision to recognize the state of Israel.  

In the matter of Israel's recognition, Secretary George Marshall and other high-ranking officials at State and the CIA were adamantly opposed.  In a series of contentious meetings as related by Clark Clifford, the State Department argued continually with Truman not to do it.  It came to a point where a furious Marshall told the president that if he recognized Israel, Marshall could never vote for him again. 

Such arguments are certainly not bad for our democratic form of government.  A wise president welcomes and solicits advice and comments from his Cabinet.  This is all part of good decision-making.  The difficulty came in after Truman formally recognized Israel on May 14, 1948, for that did not end the resistance to his decision. 

To his credit, once the decision was made, George Marshall let the president know that he would never agree with it but that he would not oppose it.  Not so with the boys in the CIA.  As Michael Doran of the Hudson Institute puts it: 

The 'deep state' worked to reverse his decision.  No sooner had Truman recognized Israel than the CIA secretly sponsored and funded the establishment of the American Friends of the Middle East.  Outwardly a 'people-to-people' public diplomacy initiative, AFME brought influential Middle Easterners to the United States, helped them write and publish books and articles, and seeded Middle Eastern student organizations on American college campuses.  It also lobbied Congress – against Israel.  AFME was a remarkable instance of a CIA-confection front organization designed to counter official government policy, in this case seeking to delegitimize Zionism in domestic American politics.

Whether one agrees with Truman or not, to undermine his decision was patently wrong.  He was the president.  And this underhanded resistance was carried out by a CIA that was created just a year earlier by Truman himself as an organization that was to assist the office of the president by merely collecting intelligence, not undermining policy.

As to why Truman created the CIA in the first place: The CIA was to serve the president by consolidating intelligence reports from numerous sources.  It was never intended to pursue its own policies.  In hindsight, however, President Truman saw that he created a monster and regretted it.  He came to realize that government bureaucracies sooner or later fall under the control of an elite whose belief is that the department is not necessarily accountable to the president or his Cabinet.  Truman lived to see his CIA creation slip the bonds as to why it was established and become a quasi-independent entity, one that refuses to recognize the voice of its master, the president, and by extension the American people.  As Truman bluntly said:

But it got out of hand.  The fella ...the one that was in the White House after me never paid any attention to it and it got out of hand.  Why, they've got an organization over there in Virginia now that is practically the equal of the Pentagon in many ways.  And I think I've told you, one Pentagon is one too many.

Now as nearly as I can make out, those fellows in the CIA don't just report on wars and the like, they go out and make up their own, and there's nobody to keep track of what they're up to.  They spend billions of dollars on stirring up trouble so they'll have something to report on.  They've become...it's become a government all of its own and all secret.  They don't have to account to anybody.

That's a very dangerous thing in a democratic society, and it's got to be put a stop to.  The people have got a right to know what those birds are up to.  And if I was back in the White House, people would know.  You see, the way a free government works, there's got to be a housecleaning every now and again, and I don't care what branch of the government is involved.

They don't make Democrats like Harry Truman anymore.  Or many Republicans, either.

What we have today is a State Department that is consistently pro-Arab and globalist in its reflexes, and that too often marches to its own drumbeat – a CIA whose incompetence is legendary yet does not blink in secretly meddling in the affairs of governments here and abroad, a politicized FBI and Justice Department, a radical EPA, and so on.

Harry Truman's situation pales in compassion to Donald Trump's.  Of course, the bureaucracies of Truman's day were midgets compared to what they have since grown into in terms of size and arrogance.  In Trump's case, highly placed people in the Deep State (FBI, CIA, and Department of Justice) actually went so far as to break the law in attempting to elect Hillary Clinton.  When that failed, they continued to try to overturn the election result, which they did not approve of.  That battle is still raging, and for the sake of the Republic, Trump has to be victorious

Harry Truman prevailed in the case of Israel, but his experience foreshadowed the general mindset of government bureaucracies.  Part of the problem here is that when the bureaucrats undermine legitimate policy or drag their feet in its implementation, they seldom, if ever, personally pay a price for their disobedience.  At most their actions are thwarted, but they live in the bureaucracy to fight another day.

As Harry Truman stated above, to have free government, every now and again, there needs to be a thorough housecleaning of the bureaucracies.  This goes under the rubric of "draining the swamp," and now it's needed now more than ever.