This breaks my heart because you can see the exact moment that Lilo realizes how important she is to Nani. She has seen herself as the burden and responsibility (“You’d trade me for a rabbit”). She worries that she takes away the good things from Nani (“Did Stitch and I make you lose your job?”).
But right here at the end. She realizes. She is the good thing. She is the ONE. GOOD. THING. that Nani wants to keep. And she’s realizing that Nani won’t get to keep her.