Political appointees should set broad policy guidelines and stay out of the way when it comes to individual charging decisions.
As for what the career prosecutors should do, they should make a case if there is a high chance of success in court. In this case, that means staying away from a jury trial where one Trumper would be enough to prevent conviction. Here’s the relevant rule::
Charge him with violating the Espionage Act, and you are handing him another big win, just like the Democrats did with impeachment.
Charge him with stealing a few papers rightfully the property of the Nation Archives, and that might get an actual deserved conviction.