Grand Juries and the Unitary Executive

I was reading an account of Robert E. Lee's indictment for treason. In May 1865, a federal district judge in occupied Virginia convened a grand jury to consider an indictment of Lee and others. A true bill was returned. I gather that no prosecutor was involved. This action created a firestorm and President Andrew Johnson ordered the indictment dismissed.

The fact that grand juries could indict people on their own at common law in cases where they could draw on their personal information and experience poses an interesting exception to the unitary executive theory. A President, of course, still retained control over bringing the prosecution. But he did not have full control over the indictment decision, which was an important one.

I am unclear if this sort of independent indictment could still happen today. The Federal Rules of Criminal Procedure do not seem to require a presentation by a prosecutor, but I do not know the case law well.