The difference here, I would think, is that the Toy Story Toys are meant to be toys. Disney Princesses may be similarly stylized in the animated medium, but you're meant to believe that somewhere off the screen they're walking, talking people. It makes sense that they'd be portrayed as people when you meet them in person. But Bo Peep isn't a person, she's a toy, so the plastic and proportions are priority to sell that.
Besides, it'd be weird for Bo Peep to be a face character standing next to Woody, Buzz, and Jessie who aren't.
