Final Choice; his will to defy destiny
How many of us are willing to choose death as the ultimate form of personal liberty? And just how many of us would able to choose the method of our departure? Kaworu's death in the manga is very different from the anime. The anime version of Kaworu died so humanity, and therefore Shinji, could survive, whereas his manga version had no interest in any of that.
He was doomed to die no matter what. Kaworu's destiny was to return to Adam, but his existence would have ended with Third Impact, because Kaworu viewed living with no individuality as good as being dead. If he chose to defy the committee, they would have terminated him immediately. So what was he to do? Dying was not a question.
The only absolute liberty left to me is that I can choose the form of my death by my own will. Nagisa Kaworu, Stage 73
Kaworu valued his freedom, even though he had experienced it for such a short amount of time. Or perhaps that was exactly why he valued it so much. He did not enjoy being SEELE's tool, and he did not look forward to their "hope" for humanity. So the last and only freedom left to him was how he was going to die. To take control, he chose to die at Shinji's hands, in a personal way that left a mark on Shinji, ensuring he would live forever in Shinji's memories. His absolute liberty was the method in which he was to die.
I believe he knew Shinji cared for him, deep down, despite Shinji acting otherwise. Because of this, I think Kaworu wanted to die at the hands of someone who cared for him, at least a little bit. So he chose Shinji to carry out his will. Even though he really didn't care for anyone, Kaworu wanted to be loved, and so he selfishly had Shinji stain his hands with another Angel's blood, forever carving this guilt and his own existence into Shinji's mind and heart.