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[Judge Ellis] . . . also asked whether Rosenstein, who oversees the probe and is considered an important witness into whether Trump tried to obstruct justice, is recused from the case.

OUCH! That’s gonna leave a mark. In the first instance, Ellis rightly demands to see the mandate Mueller received from Rosenstein - and in the second place, he asks what business Rosenstein has giving anyone a mandate in a case where Rosenstein himself "is considered an important witness.”
That last is a rationale by which Judge Ellis could simply rule that Morrison v. Olsen was wrongly decided, and that Justice Antonin Scalia’s famous
That is what this suit is about. Power. The allocation of power among Congress, the President, and the courts in such fashion as to preserve the equilibrium the Constitution sought to establish. … Frequently an issue of this sort will come before the Court clad, so to speak, in sheep’s clothing: the potential of the asserted principle to effect important change in the equilibrium of power is not immediately evident, and must be discerned by a careful and perceptive analysis. But this wolf comes as a wolf.”
solo dissent is vindicated by history and by the actions by both Rosenstein and Mueller in the present case.
That is, he could assert that the Special Counsel office as such is a rogue institution which is out of constitutional bounds.
Such a ruling would require brass - but would it really require more than the Ninth Circus routinely puts on display? Incidentally, AFAIK none of the 8 justices from whom Scalia dissented are still on the bench. I think Justice Kennedy is senior in terms of years on the Court, and he was appointed after Scalia made that solo dissent as a freshman.
Rosenstein and Mueller could appeal to the 4th Circuit, and nominally that appeal would be a no-brainer. But that could serve only as a stall, because the loser would appeal to SCOTUS - and in the nature of things, the best remedy would be for SCOTUS to ask the 4th Circuit to refuse to hear the appeal - and for SCOTUS to hear it on an expedited basis. But that is a pretty optimistic scenario . . .