In cases I have seen like this, the FBI civil rights investigation will wait until the state level investigation is completed.
Then they will compare notes and evidence with state and federal prosecutors involved.
If the feds find civil rights violations, they will offer a deal for the state to prosecute on the state level. It leaves the state no choice but to file charges.
If the state declines to file charges if the feds feel charges are warranted, then the feds will file civil rights violation charges themselves. Most of the time, state's prosecutors will prefer to handle the prosecution, and exclude the feds.
The trick is getting the two levels of govt. to agree as to whether charges are warranted. If evidence is overwhelming, then they pretty much play ball like I described above.
