Notes on the armies going into this alternative campaign and the commanders. For these purposes I will use the September numbering for the Union corps.
For the most part, the Union has suffered fewer casualties because they weren't routed, but they also don't have a lot of achievements to point to. The Confederates have suffered a lot fewer casualties and Longstreet's corps in particular is almost untouched.
The AoP's wagons take until at least the 11th to finish unloading, so I don't think Pope can simply take out the entire army - there isn't the means to logistically support it manoeuvring in the field. In addition I don't think Halleck would let Washington be uncovered, and historically the 11th, 3rd and most of the 5th were left behind.
Historically SO 223 relieved FJ Porter and Franklin of duty, Hooker was assigned to command 5th Corps and 6th Corps was attached to the 3rd; SO 224 replaced McDowell with Reno as 1st Corps commander. McClellan asked Lincoln to reconsider these, but since Porter, Franklin and McDowell were all to my understanding under a cloud from Pope then Pope will not. Indeed the drivers for these seem to basically be driven by Pope's historical report, though of course if Pope hasn't suffered a clear defeat he won't be looking for scapegoats.
I think on balance it's likely that Porter is in for it but Franklin and McDowell may not be. Of the two it's more likely that Franklin gets it than McDowell, Franklin is closely tied to McClellan.
My suspicion (and this is pretty plastic) is:
1st Corps - Would probably remain under McDowell.
2nd Corps - Remains under Sumner; no problems here.
3rd Corps - if Franklin goes down then it might be connected to 6th Corps as planned, which would make it a very big and quite unwieldy organization. On the other hand, if Hooker gets a CC spot (as with 5th Corps) then it leaves the upper command structure somewhat impacted. Kearny would also be livid if Hooker got a CC slot and he did not; something that might be interesting would actually be if Heintzelman ends up commanding the Washington defences and Kearny gets the combined 3rd-6th Corps, though of course as far as Pope is concerned Kearny has let Pope down (the same way Porter did) in the last few days.
There's a lot of variance here.
4th Corps - only one division in the DC area. Historically was attached to 6th Corps; would presumably be attached to another here. Note that Couch as an AoP divisional commander is actually surprisingly senior, he's just below Hooker and above Richardson.
5th Corps - Porter's almost certainly going down as Pope blames him for not catching Jackson on the 28th.
6th Corps - see above with 3rd Corps. If it retains an independent organization then I think Franklin remains in command, though see below.
9th Corps - interestingly has a command structure full of - at the time - very senior generals. Stevens isn't dead because no Chantilly, and since Reno was historically considered for a corps then 9th Corps might be mined for senior generals to replace anyone who's considered unworkable (like Porter or Franklin?)
11th Corps - historically pretty badly shattered by 2BR, though the command structure was largely intact. Sigel actually did pretty well historically.
12th Corps - historically Banks was sick, which would leave Williams in command unless someone else takes over.
Pope's historical reports, among other things, scapegoated McClellan for not sending him the veteran troops from the AoP (though Pope's count was very off, he thought that 2nd, 3rd, 5th, 6th Corps combined was only about half the AoP) but based on this Pope might well aim to take out veteran units and not bulk out his army with new ones. Combine this with the desire by Halleck to have veteran troops to defend Washington, and the supply limits, and there's at least the potential for the "Army of Maryland" to actually be surprisingly small - it might well not be as big as Lee's.
As for Lee, his main concern is that he doesn't want to give DH Hill a "corps" command and so will probably operate his army in more than three components - his historical set up was Jackson's wing, Longstreet's wing, a wing under McLaws of his division and Anderson's (a wing which is basically a quite big Federal corps) and then a small division under Walker and what amounts to a binary corps under DH Hill because DH Hill's division is huge.