First, Marcy's orders to Pope were not unambiguous because they contained the formula "your command" and Pope has (a) lost touch with his command and (b) proposed a new command to consist of Banks, McDowell, Reno, and Hooker and may have been awaiting word on the approval of this field army from Halleck.
Second error: an injustice to Rafuse. I had said
Rafuse [makes] what I believe is an inference – that Lincoln and Halleck had decided to liquidate the AoV and transfer its commander before McClellan issued his command to Pope and that Pope’s reaction to McClellan’s command then triggered the disclosure of some Lincoln/Halleck decision that had already been taken but somehow not communicated.In rereading the events surrounding Pope's official report of the recent battles, I think an inference may be fairly taken, given the furor around Pope's report the previous evening and in the morning. Rafuse likely has the sequence right - the stage was set for adverse action against Pope; Pope's reaction to Marcy's orders may have triggered a decision taken earlier in the day.
On the other hand, orders to report to Stanton for assignment also indicate that the decision was not ripe. (Let's note also that Pope's report - at the center of the furor - was published against the wishes of Lincoln, and Halleck referred to that action as a component in the decision to relieve him in correspondence in October.)
In refreshing the crisis timeline, I noticed that Sears without notation in his Civil War Papers of GBM, says "Earlier that morning [Sept. 5] President Lincoln directed GBM to take command in the field against the Confederate invaders in Maryland." This is in a category of nonsense so foolish it can only be called "Searsian." Another such is Sears' willfull misdating McClellan's telegram to Lincoln on Sept. 13 as midday when it was sent that evening at midnight. (Rafuse has fallen for this too.) Another is Sears' comically inept account of Franklin at Antietam (see here and here). It goes on and on, but so must we.
The most intriguing discovery in reviewing the timeline was in Civil War High Commands by Eicher and Eicher. They carry Pope as commander in the Northwest from 6 September, which is per orders, but they leave him as commander of the AoV until September 12. Likewise, in their army chronology, they do not liquidate the AoV until September 12.