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.
It is possible to save Anakin’s confession if you cut every line in italics:
INTERIOR: TATOOINE, HOMESTEAD, GARAGE - DAY
PADMÉ comes in with a tray of food and a blue drink. ANAKIN is standing at a workbench, repairing a part of the speeder bike.
PADMÉ: I brought you something. Are you hungry?
ANAKIN does not look up from the bike part.
ANAKIN: The shifter broke. Life seems so much simpler when you’re fixing things. (as PADME puts down the tray) I’m good at fixing things…always was. But I couldn’t…(stops working, finally looks at her) Why’d she have to die? (sighs) Why couldn’t I save her? I know I could have!
ANAKIN walks offscreen. He continues to walk away from PADME.
PADMÉ: Sometimes there are things no one can fix. You’re not all-powerful, Ani.
ANAKIN: Well I should be! Someday I will be… I will be the most powerful Jedi ever! (turning back to her) I promise you, I will even learn to stop people from dying.
PADMÉ: (concerned) Anakin…
ANAKIN: It’s all Obi-Wan’s fault. He’s jealous! He’s holding me back!
ANAKIN hurls the wrench across the garage. It clatters to the floor. ANAKIN turns away from PADME walks across the garage. PADMÉ stares at him.
ANAKIN: …and not just the men, but the women, and the children too.
The camera zooms in on PADME.
ANAKIN: (offscreen) They’re like animals, and I slaughtered them like animals…I hate them!
ANAKIN’s lip quivers, then he turns away. He goes to the ground. PADME watches him. She sits by him.
PADMÉ: To be angry is to be human.
ANAKIN: (shaking his head at her) I’m a Jedi. I know I’m better than this.
ANAKIN starts to cry softly and PADME puts her hand on the back of his neck. She strokes his head as he cries.