Since when does the FBI need presidential permission to charge someone? Or has the counter-order already been issued?
The FBI investigates crimes and, when the evidence warrants, makes a recommendation to the Justice Department. It is up to Justice to bring an indictment.
This is no different from local law enforcement. The police don't issue indictments. They present evidence to local prosecutors. The city, county, or state prosecutors bring the indictment.
Separation of powers and all that.