No he saw though the Lie, Sakura probably wants to say she likes Naruto, but that was not the real intent, she wants him to stop chasing Sasuke.
And Naruto now knowing the clear situation with Sasuke as told by Madera, and what Madera plans to do with Sasuke, he is not going to stop chasing him, and probably that's also why Yamato was all like What hell are you...
and that look on Kiba's face, and that flashback scene with the Konoha 11 or something.
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so hmm whats the real deal then. anyway before he responds to Sakura on how he wants to Naruto has to formally respond to Hinata first; whatever re decided to do.