He does not love Malia. He never did. He’s just thankful because she loves him. No one ever loved Stiles. No one put him on #1. Malia does and he’s just thankful, but he does know it’s unhealthy and that she’s no good for him. He’s just too sweet to let go on her and he’s also kinda desperate. He’s not the type to dump someone randomly. He also wants to protect her from going to Peter, but since Peter is locked up, it’ll be easier for Stiles to let Malia go.
He doesn’t love her. He knows it’s no good. He loved Lydia and soon he’s going to let Malia go, because he realizes it’s not his job to stay with her so she doesn’t fuck up.