I think that the key to understanding how padme could marry anakin even after what he had done to the tusken raiders, how she could plead with him on mustafar to come with her even after his massacre at the jedi temple, to me it's all in that deleted scene in aotc when she and anakin visit her home on naboo, when she shows him her bedroom and talks about the little boy in the holo on her wall. how his planet was dying and he had to evacuate, but his species could not survive on another planet, and so he died in her arms, with padme unable to save him.
the thing about padme is that she wanted to save everyone in the universe the way she wanted to save that little boy. as the queen, she was desperate to save naboo, she wanted to save her world. as a senator, she wanted to save the galaxy from war. and by mustafar, anakin had become her entire world.
when padme looked at grieving, furious anakin after shmi's death, all she saw was someone who needed her desperately, someone who needed to be saved from his own pain and grief. anakin had the deepest, most all-consuming, all-absorbing kind of need--he was someone who needed to be saved from himself.
and padme needed to be needed in that deep, primal kind of way. because padme had always been desperate to be someone who could save the ones she loved.
