Even if she wants to free him from the Seal, by doing so just by itself it would doom the world, so that can't be what she's after. I mean, I CAN see that's what the ultimate bad is trying to get her to do without her realizing the ultimate outcome of her actions, and it's definitely something it would do(the road to hell IS paved with good intentions after all).
Yes, her goal is to rescue Makoto from his predicament, so the other thing to think about is how far is she going to go. To sacrifice the world would go against his own wishes, which she has to know so it can't be what she's after. Then again she awoke to the Fool Arcana, and over the course of Makoto's journey he awoke to the Universe, so maybe a Fool can take his place...
Of course all this implies that if he's able to free of the Seal he can just live again, which is another leap since there presumably was a Makoto dead body.