Game of Thrones thrives on secrets, but one thing that certainly isn't a secret: Daenerys Targaryen and Sansa Stark don't exactly see eye to eye. From the moment the Dragon Queen arrives at Winterfell, she and the Lady of Winterfell are at odds, if very polite, passive-aggressive odds. Dany is frustrated by the lukewarm reception she's getting, while Sansa doesn't understand why Jon would bend the knee and give up what the North has worked so hard for. So far, the two women have kept their differences mostly under the surface, but could all that change soon?
Sansa now knows that Jon is actually a Targaryen heir — and not just that, but half-Stark, half-Targaryen and the son of the previous eldest Targaryen heir, making him a more legitimate claimant to the Iron Throne as well as a man the North would follow. Sansa already isn't thrilled with the idea of Dany on the throne and taking away the North's independence again, so it's possible that she'll push for Jon to claim the throne instead. It would certainly be very dramatic for Jon to have to choose sides between the woman he's in love with and the woman he loves as his sister.
Is it possible that the real final conflict will be between Sansa and Dany, rather than between Cersei and Dany/Jon/whoever else? It's possible, but probably not the most likely conclusion. Cersei has been set up as the ultimate, final villain of the series, so it's more likely that, whatever the final confrontation is, it will have Cersei at the center. However, that doesn't mean that Sansa vs. Dany won't happen in some capacity. Given that neither woman seems likely to budge on their respective positions, they're almost certain to come into major conflict about the future of the kingdom, and Jon is almost certain to wind up in the middle, since he's very close to both of them and is politically important.
The possibility does exist that Dany could die and that Sansa would be responsible, but it seems unlikely. Sansa is tough, strong-willed, and resilient, but she's only ever been violent toward the most evil of characters (such as Ramsay Bolton). While she clearly disagrees strongly with Dany, she also wouldn't be likely to put the Dragon Queen on the same level as someone like Ramsay, who truly deserved a violent end. If Sansa did have a hand in causing harm to Dany, though, it would almost certainly be indirectly or discreetly: she's more of an Olenna Tyrell than a physical fighter like Arya or Ser Brienne. We've only got two weeks left to see how this rivalry between Sansa and Dany plays out against the backdrop of the final battle for Westeros!