All the federal agencies can do is investigate and report to congress. It would be up to congress to do something about it. And a lot of them are just as compromised as Trump. The ones who aren't, would have to raise enough noise, and get enough people to care, to do something about it. As far as his cabinet, the congressional confirmation process is supposed to serve as a check on presidential nominations. That's why he is trying to go around it, and make recess appointments. He can use those to temporarily bypass Senate confirmation to avoid that safeguard.