It is not fraud, waste and abuse they are against, it is destruction of the agencies "accused" of doing that.
To begin with, there is not one single agency in the U.S. and for the past 70 that cannot be accused of having fraud, waste and abuse occurring and that is even more real when the Republicans are in office than when the Democrats are:
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Secondly, you do not go and attempt to stop it in a dictator-like way but in a Democratic way, meaning that first you investigate it, then you make a valid and supported accusation and then you prove it in court.
All of that is being put aside by Trump, starting with the fact that they are making accusations and not providing proof of anything. With Trump and Musk being proven liars, such accusations should not be taken at face value.
Having said all of that, if found guilty, you then prosecute those that are guilty of the charges but you do not prosecute everyone in those agencies, or even less the agency itself as there is a lot of good being done there, aside from the fact that they provide needed benefits as well as jobs for many Americans.
The idea of finding fraud, waste, and abuse is a good one but not this way!