Do you think the Justice Department should prosecute people they believe to be innocent? If not, it seems that every prosecution is an expression of the view that the accused is guilty, and by allowing the JD to proceed, the President is expressing approval of the view. Can you please point out the error in this logic?
The potential source of error is the assumption that the president has the authority to stop a prosecution (short of the pardon power). I say "potential" because a "unitary executive" advocate would claim this is true, and it is becoming more true during the second Trump administration, although it was notably false during the first one. [In prior administrations, including Trump I and Obama, the DOJ appointed independent counsel precisely to prosecute cases the president would have disagreed with prosecuting.]