Well, it seems like Natsume has been reincarnated, but for some reason, Harutora had to leave her behind, right? The obvious answer is, he did something taboo, forbidden, and there seems to be some unfinished business with the Taizan Fukun ritual, which makes it logical that he make his escape so that he could finish what he started.
Also, it seems logical for Natsume to be left behind like that...I mean if you think about it, Harutora must have sacrificed something bigger than life to dabble on something as taboo as resurrecting the dead--which in any other anime I've seen--is more seriously labeled as evil magic.
Given Natsume's character, she wouldn't have allowed Harutora to do something like that--in fact, she had already voiced her objections back when Suzuka attempted to use the same ritual. This reason alone puts Harutora in a precarious situation where he must resurrect Natsume against her consent. Her objecting to the process might only complicate things and distract him from his--should we call it romantic or obsessive--goal of prolonging her life or resurrecting her completely as a normal human being.
If I were Harutora, it would be too frightening to face someone you love only to tell her that her life depends on certain `uncertainties' including the help of other-worldly gods, demons, or what-have-you and doing all that for what reason? For love that is pure and true? I don't think Harutora even has the slightest understanding of what he truly feels for Natsume, though the fact that he does feel something profoundly and frighteningly deep is itself beyond doubt...
Having said that, I'd probably put on my best sneakers and prepare to run, if only to save myself from the embarrassingly disturbing explanations--and confessions--I'd have to make to satisfy Natsume's excruciatingly probing curiosity..
Finally, if Harutora had to sacrifice himself eventually, as that could be the only possibility left to complete the ritual, I'm sure he wouldn't want to do it right in front of her. He knew what that felt like, having witnessed Natsume's death first-hand, and being the cause of it too. I think he wouldn't hesitate to give up everything for her, but just so he didn't have to feel so bad about it, he could do that on his own, like some supreme, heroic sacrifice that nobody should interfere with, especially Natsume, who might reject that offering--a rejection that to Harutora would be even more tragic because as is surprisingly obvious, he's just that kind of guy who doesn't know when to give up. Or maybe it's just the case of stubborn true love?
What's clear is that he is unwilling to go on with his own existence without Natsume, as is obvious when he touched the missing pentagram on his upper left cheek right after the death incident and mourned her loss crying out her name repeatedly--something he was only able to do when he was imprisoned by Kurahashi/Yashimaru in the Onmyou Agency headquarters.
The feeling that somebody has to die somewhere down the road towards Natsume's final resurrection depresses me as this seems ominous from the very start... That Harutora might have to figuratively die to give way to Yakou's complete awakening as a means to perfecting the forbidden ritual is a strong possibility, then there's the more poignant possibility of Natsume giving up her life to free Harutora from the obligation he had set upon himself to resurrect her, especially when she realizes eventually the depth of his sacrifice... I don't know which way the story might go, but there's bound to be something romantically tragic in the end... and it almost makes me reluctant to know how everything might really turn out... huh, talk about 50 shades of reincarnation, right?