One of the darkest fears I have is that only the body of the agency is gutted, but the head remains alive.

By which I mean, if we have this:

FBI: The power to investigate anything.
CIA: The power to spy on anyone.
NSA: The power to surveil the internet.
TSA: The power to search and seize anything at a border.
DMV: The power to be boring and tedious and make people wait in line.
IRS: The power to steal money.

If they only take away the employees and structure, but keep the Authority and Power intact, then they now have pocket-sized authority-tickets that let them do the things that the agency once did instead.

And I highly doubt they'll give up their power! They will want MORE power - And will they will drain it from anything they want and keep it for themselves in some/any form?

Furthermore, they can always grow these agencies again - But won't they grow it with only their own people, to deliberately corrupt the government?