Arya can absolutely kill Jaime, take his face, then take our Cersei, in very quick succession.
I think what Cersei was told will have her keeping a watchful eye on Jaime, but she'll feel comfortable as he does things throughout this season to assuage concerns, then bam, just when she's comfortable that it isn't him, he'll be killed and will lose his face to take our Cersei, when she least expects it.
Plus, the bald eunuch has laid the tracks that valnoqar can also be a female. And Jon has referred to her as the "little sister" throughout.
"until there comes another, younger and more beautiful, to cast you down and take all that you hold dear"
What does she hold dear at this point? Jaime and power. We all thought it was Dany, but it could be Arya too.