I have thought for some time that many departments of govt. are so infested with deep staters that the only solution is to recreate department after department. Get rid of the old employees as best you can considering union regs and how hard it is to get rid of Civil service employees.The most practical solution is exactly what you said: recreating government! We have the right potus to do it.
The University Professors often are there to promote Socialism.
Gubmint unions were created by an EO, he should be able to decertify them with a current stroke of the pen.
Retire positions as they are fired, and defund and abolish certain departments and agencies if they have no real useful function. Any federal depts and agencies which have redundant counterparts at the state level should be abolished by whatever means necessary.
Transfer those useful functions to better agencies (like the Federal Marshalls from the FBI)
Allow fired rank-and-filers to re-apply for positions using their skill-set, but subject them to "extreme vetting" like party affiliation, US loyalty, and deep individual interviewing. We don't need any more RATs in the "deep state".