Judges can’t really force prosecutors to prosecute.
In this case, Judge Sullivan, who is mightily annoyed at Flynn, has a little room to maneuver, but not much. If he wants to reject aggressively the DOJ’s motion to dismiss – that is, if he wants to suggest openly that the the DOJ is acting in bad faith (which it is) – he will have to do a fair amount of work arguing against precedent that would otherwise be controlling.
Short of that, he can do two other things: dismiss the case in a way that allows a future DOJ to take it up again; or at least try to embarrass Barr by asking for a detailed explanation.
Obviously, I can’t say if he’s contemplating doing any of this work – nor can I say when he will announce his decision.