I think the rule you are citing applies prior to the entry of a plea and it still requires the permission of the judge
Note to Subdivision (a). 1. The first sentence of this rule will change existing law. The common-law rule that the public prosecutor may enter a nolle prosequi in his discretion, without any action by the court, prevails in the Federal courts, Confiscation Cases, 7 Wall. 454, 457; United States v. Woody, 2 F.2d 262 (D.Mont.). This provision will permit the filing of a nolle prosequi only by leave of court. This is similar to the rule now prevailing in many States. A.L.I. Code of Criminal Procedure, Commentaries, pp. 895–897.
And has been pointed out by Ginsberg last week, citing her previous opinion in Greenlaw [Scalia concurring] where the government chooses to prosecute the case is done. The judge has no discretion to continue a prosecution in the place of the government, to wit, the DOJ.
Ginisberg made clear that as the neutral party the judge cannot take an interest in or prosecuted case that the DOJ will not prosecute.
On May 7 2020 AJ Ginsburg writing for the court in a 9-0 decision in UNITED STATES v. SINENENG-SMITH reversing the 9th circus stated
Instead of adjudicating the case presented by the parties, however, the court named three amici and invited them to brief and argue issues framed by the panel, including a question never raised by Sineneng-Smith: Whether the statute is overbroad under the First Amendment. ....
The Nation’s adversarial adjudication system follows the principle of party presentation. Greenlaw v. United States, 554 U. S. 237, 243. “In both civil and criminal cases, . . . we rely on the parties to frame the issues for decision and assign to courts the role of neutral arbiter of matters the parties present.” Id., at 243
Even more damning in this case is what Ginsburg wrote in the cited Greenlaw case where she said:
“[o]ur adversary system is designed around the premise that the parties know what is best for them, and are responsible for advancing the facts and arguments entitling them to relief.” (Scalia, J., concurring in part and concurring in judgment). As cogently explained:
“[Courts] do not, or should not, sally forth each day looking for wrongs to right. We wait for cases to come to us, and when they do we normally decide only questions presented by the parties.Counsel almost always know a great deal more about their cases than we do, and this must be particularly true of counsel for the United States, the richest, most powerful, and best represented litigant to appear before us.
And Ginsburg continues in Greenlaw: This Court has recognized that “the Executive Branch has exclusive authority and absolute discretion to decide whether to prosecute a case.” United States v. Nixon, 418 U. S. 683, 693 (1974)
So holdeth Ginsburg and her colleagues.
In this case, the United States has withdrawn from prosecution and sought to dismiss.
Judge Sullivan cannot continue a prosecution in place of the DOJ.
And the controlling case in the DC Circuit is Fokker In that case the DC COA held: "[T]he `leave of court' authority gives no power to a district court to deny a prosecutor's Rule 48(a) motion to dismiss charges based on a disagreement with the prosecution's exercise of charging authority." United States v. Fokker Servs. B.V., 818 F.3d 733, 742 (D.C. Cir. 2016).
The case further held:
The Constitution allocates primacy in criminal charging decisions to the Executive Branch. The Executive's charging authority embraces decisions about whether to initiate charges, whom to prosecute, which charges to bring, and whether to dismiss charges once brought. It has long been settled that the Judiciary generally lacks authority to second-guess those Executive determinations, much less to impose its own charging preferences.