If you want to show Anakin and Padme captured why not cut to the chase and just show them being captured, you don't need the the droid factory at all just Anakin and Padme entering the lair and then perhaps Jengo and the battledroids coming to capture them and replace it with the deleted conference table scene and trial.
That way you don't have to balance a bad CGI Threepio head swap against footage which shows a physical Threepio missing an arm appearing in the same cut (the two hardly resemble the same character).
The droid factory sequence adds nothing to Luke or Anakin's strands of the story in this new context, we already know their are droid factories on Geonosis when Obi-Wan is investigating them.
The conference interogation conveys that they are captured, what the Seperatists want and that they are to be put to death for not joining them.