I would argue that the character of the young Daisy Miller was an innocent flirt rather than a manipulator. She was full of life, of freedom, of sincerity, and of grace, and she was beautiful, carefree, charming, and certainly ahead of her time, but she was far from being a manipulator. She had "a great deal of gentlemen's society," as she herself pointed out, but she was unpretentious, "unsophisticated," and "completely uncultivated," as Winterbourne described her, so it is possible to say that she acted naturally, not in a manipulative way.
This can also be confirmed in the passage that narrates the moment when they both met: "... (Daisy) was a coquette; he was sure she had a spirit of her own; but in her bright, sweet, superficial little visage there was no mockery, no irony." This, once again, indicates that she was honest and straightforward, and far from Machiavellian.