The 'deep state' is no joke. Mathematically, let's say workers at each level down carry out 80% of the boss' demands (which is a pretty high assumption), after 4 levels, the top executive only gets 40% of what he wants done, done. When you have high level officials and minions actively work against your agenda (as Veritas videos showed), your direct orders don't go much further than the lawns outside of the White House.
This highlights the importance of Trump running a few high-profile prosecutions and putting a few heads on spikes. He cannot do it without DoJ carrying out his commands and Sessions is the biggest swamp creature. But it's all wishful thinking: Trump cannot restore the rule of law because he is also swampy, having publicly admitted obstruction himself and slew of opaque activities.
Emperors in China learn their Machiavellian art from a number of classics, and they always learned to tolerate a certain degree of corruption. It's much easier to control a bunch of corrupted officials because you can hold a sword over their heads and keep them in line. The clean ones have way too much moral authority to be destroyed willy-nilly.