She kisses him and it doesn't feel wrong. She knows now, of course. She knows that the bond they share goes through mind, through body, through blood.
She doesn't care.
Kissing him is like coming home.
She stood by and watched her first home utterly destroyed by the Sith and she could do nothing.
She had sworn never to be that helpless again.
But really, it only makes sense, what's happening now. After all, the Jedi and the Sith have always been in perfect opposition to each other, and since the Sith demolished her first home, does it not make sense that the Jedi try to kill her new one?
She doesn't cry as she watches him become more Jedi and less Luke, but she stands by and watches and remembers the way he used to be.
And she plans.
She is not a helpless captive this time, and she does not care if the Jedi will be gone from the world forever.
They have never mattered to her anyway, and in the end, they are as fragile as the Force they depend on.