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Yes when one thinks in terms of the deep state as being the vast government bureaucracy, then it has both positives and negatives. The positive, of course, is that the government functions 24/7 and 365 days a year (even with a government shutdown) despite changes in leadership at the top. Just about every president, Republicans and Democrats, have tried to trim the organization to be more cost effective and efficient, and all run into resistance because all those initiatives translates into jobs lost.
However, as you noted, no president has time to micromanage the 4 million plus employees worldwide. That's why it is so important to hire competent and experienced people for his/her leadership team (including ambassador posts) to be able assess and reorganize staff as necessary to eliminate deadweight or add people where necessary in a changing world, and more importantly to earn their trust.
Furthermore, when it comes to implementation of policies, it is important for the president and the many competent department heads to communicate a vision and strategy that is well thought out and that can be embraced by the many employees down the line and not undermined. An authoritarian president like Donald Trump shows his weaknesses by his outright ignorance of government and invites contempt by the deep state when he clings to campaign promises that were poorly thought out in the first place...e.g. building the wall, trade deals, Iran nuclear deal, climate change initiatives, immigration and more.
In Trump's first address to the CIA, for example, he showed just how little he knew, and he certainly didn't earn any respect from the dedicated employees there. Ditto for just about every other organization. He got off to a bad start because he was unqualified to begin with, an exceptionally bad businessman who tried to bring his bad business practices into managing the government. The only thing he was good at was lying...and being a fuckin con artist.
What we have with the Trump administration is a kakistocracy, a form of government in which the least competent worst persons are in power.