I still do not believe there is a "deep state". And the resistance you speak of is a good thing. Political appointments can be made for a variety of reasons that have nothing to do with competence. The civil service is staffed with experienced professionals who know how things work (and don't work). If some edict comes down from the cabinet, and it is idiotic, it's really the job of the professionals to say "this is stupid, you may want to rethink that". Ultimately, the Cabinet person may get their way. But it's part of the job to let them know they're being dumb (or even illegal).

I can't tell you how many times a manager would try to tell me how to do my job. I would nod, and then do it the right way anyway. I got results, so I didn't get in trouble. (If I didn't get results, I probably would have been put on a PIP. But I knew my job, and how to do it. Managers and VPs generally didn't.)