The DOJ/FBI cannot investigate itself. It is the quintessential example of when an independent investigator is required. They justified it many times in the past based just on the prospect that the Executive could interfere with an investigation - but this is a case where the investigators themselves are the target of the investigation. IMO, no way to resolve this but by a 2nd SP.
Even assuming you are right and the DOJ could do it, they would face non-stop charges of being politically motivated by the Executive branch. To avoid the appearance of meddling as well as the accusation of political motivation, it needs to be independent.
Do these independent counsels ever come up with anything that justifies their existence?
The one I remember is Ken Starr; it went on interminably and in the end only pleased those who already despised Clinton.