User blog comment:Samium/Buster Call on Enies Lobby (Aokiji's motive)/@comment-3560963-20160531075754

Actually, Aokiji DIDN'T want her killed. Not yet, anyway. That's the whole reason he spared her life the FIRST time as a final wish he granted her only friend at the time (I honestly forget his name).

And technically speaking, HE didn't want her dead, just the rest of the World Government. For reasons I frankly don't understand myself. She didn't commit any crimes, and all they're doing is censoring the truth of the world. Even Aokiji knew that, so much so that he leaves the Marines after the Marineford Arc.

As for why he changed his mind, it's because, as much as he didn't want her dead, Aokiji was starting to have his doubts. As anyone would have given Robin's undeserved track record. But when the Straw Hats practically stared down the barrel of the World Government's guns, he made sure to spare her life after they escaped.