I love how what you say about MPDG's having agency and being integral to the narrative applies to 'Looking for Alaska'. Alaska is the MPDG of Miles dreams and in the After section he does kind of appropriate the meaning of her actions, like he makes her death all about him. Green's narrative kind of does as well, by creating a hero who sees his mysterious female friend die and just happens to be totally preoccupied by last words the death, that kind of furthers Miles own journey as he tries to navigate life and death.

At the same time, outside of Miles' own head Alaska's death is so not about him at all, it is all about her and I guess it is her (tragic) way of using her agency in this narrative. And although the reader can't really get close to her because Mile's and the narrative's attachment to her as a MPDG, blocks us from seeing more of her even through the Captain's eyes, she does have agency in the Before section. We can kind of see, from everything Miles doesn't understand that she is off having a life that doesn't relate to him at all, even though he continues to...not exactly use her, but like to draw lessons from her, rather than be seriously interested in finding out about her.

Tangent note: Although I know there are some really skeevy representative issues of a narrative having a guy use a girl's death to further their development, I think it's also pretty common to find people naviagting their own lives through other character's deaths in novels (and films) because that's how we react to death so often - it's all about us.