Two stories provide an interesting picture of what may happen between Trump and executive branch agencies. The Bloomberg story about ferreting out anyone working on climate change, and Question 27 on this document suggest the obvious tension between a Republican administration and EPA employees, as well as Energy Department employees working on climate policy, but that is normal. What is not normal is the likely tension between Trump, the CIA and other intelligence agencies because Trump is still denying that Russia had anything to do with the DNC hacks or any involvement in trying to help him get elected, and he is harshly criticizing the CIA for their reports. He is simply asserting that they are the same people who got the Iraq weapons reports wrong.
Um, not quite. First, the Iraq reports were written by separate people within the intelligence agencies than the computer people. The head of the CIA during the lead-up to the Iraq war was George Tenet, who is long gone. Much of the analysis of the Russia hacks was probably done by the NSA as well, not the CIA. The NSA had nothing to do with Iraq, though, because that's just not their thing. So, no. Not the same people. Not the same analysts, and not the same heads. Then, there was the fact that the Bush administration distorted reports over, for example, the aluminum tubes and the supposed uranium from Niger... No. Let's call bullshit on this.
Executive branch tensions are normal. EPA employees are bound to be in tension with Republican presidents, and CIA employees are bound to be in tension with Democratic presidents because of general ideological dispositions. What is not normal is for the CIA to have this kind of tension with a Republican president, much less to start with it.
And normally, these tensions are mitigated by civil service protections. It is hard to fire an executive branch employee. We generally don't want the full power of the executive branch to operate as the personal machinery of the president to avoid, well, just imagine.
Could that go away? It would take legislation. Would Trump like to eliminate it? Absolutely. His catch-phrase is "you're fired!" It would have to overcome a Democratic filibuster in the Senate, though. That would require the Senate Republicans to go nuclear in order to hand Donald Trump a hell of a lot of power. Would they do it? I'd bet against it.
Consider the select intelligence committees. Their hearings are not public, obviously. However, just imagine what those briefings are going to be. With what Trump is saying now publicly, what do you think the CIA is going to say to Congress during hearings? Back-channels matter, even if you don't see them.
Remember all those endorsements Trump got from Congress? Yeah, me neither. Paul Ryan is happy about the fact that he no longer has to worry about shutdowns, debt ceiling negotiations, etc. McConnell too. But, they don't want to hand Trump any more administrative power than they have to.