Why not keep the whole garage scene, with the exception of Anakin saying that he killed the women and children?
This way you set up the plot for ROTS, keep Anakins conflict and regret about the slaughter and Padme doesn’t appear to be a hypocrite, because there is obviously a big difference between killing innocent children and the murderer of your mother.
He kills children in both instances. Neither are more or less innocent than the other, and Padme does not care in AOTC. There’s no way I’m reinstating that scene.
About the droid factory scene… I really am of two minds. I will have to mock it up and see how it plays and make an honest call about it.