Just hit VS. The Alt Sel should already be on 2000ft for the Missed; the aircraft will maintain its current RoD before levelling at 2000ft.
Laterally, the Loc will stay active. You can then change the lateral mode as you pass the MAP.
Configuration wise, you can get the gear up even though you're still descending. A change of Flap will command a corresponding change in FMS speed.
Yes, you could take the AP out if you want, but not difficult to 'manage' the automation to keep it smooth.
We use a similar technique to level using the automation when circling.