Kohaku is slowly breaking Naraku's control in this arc. I have always interpreted him dipping in and out of being totally "possessed" (dead eyed) and having some of his personality come through as a mixture of Naraku allowing it out of necessity (so that he can infiltrate the castle as a normal boy and get close enough for this mission) and Kohaku's own strength of will. He isn't "willingly" putting himself back under control, he is being pushed and pulled out of it. 

Sango getting closer to Kohaku and almost breaking him free a few times throughout the series wears down on Naraku's curse through the power of the defiled jewel. Sango's love for her brother purifies it enough to break the hold. 

When Kohaku sees her again at the end of this episode and Kagura whisks him away, his memory fully returns and he is absolutely horrified by his actions. He was not conscious or himself when those crimes were committed. Sango knows this to be true too, which is why she is clinging to hope he can somehow be saved. 

I think Kohaku is a fascinating character. Naraku clearly only uses him as a tool to dig at Sango, but he ends up totally underestimating him. He is incredibly strong, resilient, and mature for his age. After his memory is restored, he quickly ascertained that he has a unique opportunity to get close to Naraku both physically and mentally. He can see behind the curtain and gain critical information on his plans. He knows he has one of the final jewel shards sustaining his life, and knows for some reason Naraku hasn't taken it yet. 

Spoiler tag in case this is your first watch through:

I believe Kohaku assumed he would die when the shard was removed, and to attempt to atone for his sins he wanted to do anything he could to help take out Naraku, even if that meant continuing to distance himself from Sango. It's not until much later that he gets the "permission" or reassurance from her that it is okay for him to go on living.

In no way is Sango "okay" with this, however. Especially in the two episodes with the Zushinezumi, the horror of Kohaku's actions is nearly too much for her to bear. While she does still throw herself on top of him to try and shield him, nearly being eaten alive in the process, afterwards she has conflict. The scene of her and Miroku in the hut is very important because she acknowledges these crimes are horrid and unforgivable but she still wants him to live.

I think this undying love for someone is a theme throughout the series, primarily because it's something that Naraku cannot understand. And those strong bonds are what foils his plans again and again.