Hot take here: I think this is all okay. It could be worse since I actually envisioned the MC finding his little sister in someone else's arms at some point. So he gives in to a beautiful nice girl he knows well enough that relentlessly attacks him. How can a young hormonal high school boy not submit eventually? Sure, he's got some vague romantic mutual understanding with, oh right, HIS SISTER. I'm not about to rant about incest not being okay, because incest is wincest as far as fiction goes. But real high school boys aren't exactly known for their faithfulness and ability to resist temptation.
Besides, it's not like what he did is a sin. Akiho seems to be a genuinely good girl, even if she's being "bad."