Maybe Applebloom understands why this plushie is there and that it means that Applejack missed her so much in her time of absence that she couldn't resist cuddling with a plushie of her? Maybe she's actually happy about that because this is a sign for it how much her big sister loves her? If someone keeps a plushie of you for the time you aren't here with him, then it's a sign of adoration and love. There's nothing creepy about that.

You're alienating something very positive and lovely, because you imagine all sorts of horrible things in your head and because you project those things on it. That's all there is to it.