The Pin's Head
Disclaimer: I do not own Will, Lyra, or anything remotely related to His Dark Materials, all of which is the exclusive property of Philip Pullman. Except maybe the movie, but let's not speak of such despicable things.
If there is any part of Lyra that is still pure, she thinks it would be in Pan, not in her.
Pan has never really accepted Kirjava's absence, and it shows in the way he spurns intimate contact with Lyra's lovers' dæmons, and even now won't do more than touch noses with Astraea, William's dæmon. Then again, Pan is Lyra's soul, and deep down Lyra hasn't left Will in her past at all.
William keeps his distance most of the time, cool and shy and unobtrusive, with that unsettling likeness (and yet complete unlikeness) to Will. He is very rarely out of character, and that makes it very difficult to remember that he is not, which in turn gives Lyra grief whenever she forgets and he acts just a little different and reminds her again.
Like when he touches Pan.
He is good about keeping his distance, or he was, but then he does something out of order and she flinches away from him and he sees it and he hurts. She can tell that he hurts, even though he doesn't say anything.
She is sorry for that. William is a good person.
He just isn't Will.