Just realized that since stiles being taken happens in an instant, Lydia won't have enough time to cry immediately which means the test below her eye right as he is taken is from his confession/ telling her he loves her
Well, and also knowing that he was about to leave her :)
But yes, I have to agree. I think something settled inside of Lydia when he said that to her. Something made her go “oh, yes, okay. Everything’s going to be okay now. He loves me too” before remembering that it isn’t because Stiles is gonna be gone.