Setting aside that this is just generically bad, the pretense of the last few chapters doesn't make a lot of sense. We're given the shocking reveal like that explains everything, but it doesn't explain anything. If anything, it just highlights that Aki is running away, she's doing the same thing their father did but trying to rationalize it away, as though that makes sense. And the fact that they meet at the end and that final line makes it pretty obvious they aren't reuniting and it really only serves to highlight the problem with that way of thinking.
That is, just because you've deliberately separated-- not only without consulting the other party involved, but making a unilateral choice based on the pretense of knowing 'what is best' which is one of the most cruel ways you can hurt another person --it doesn't change the situation, what you've already done, and what you know in your heart of hearts. All this has done is used a convenient excuse to run away rather than faces the consequences of your actions and in so doing trading the potential for external pain when others judge you for attempting to live in the 'sin' of your socially unacceptable life choices, for the guaranteed internal pain of deliberately hurting not only yourself but the other person and having to live your life knowing that you're denying each other not only who you are, but the comfort and strength of being together and facing your choices head on.
Ultimately, there's little doubt that an incest couple would face hardships attempting to live their life together, but that is the consequence they accepted when they crossed the line and by running away from it Aki only serves to wound not only herself, but particularly Sora who she claimed to want to protect, more deeply and thoroughly than the slings of their taboo lifestyle could likely have ever done. And if this were real life, it would likely show him that he could never truly rely on her, that she's not woman enough to own up to her choices when it really counts and that's as far as her love for him goes. And more than that, it would likely cause him to resent her for her part in allowing things to escalate the way they did if she wasn't willing to accept the consequences and it would be well deserved, she did something that can't be taken back.