He was aware that the result would be different from the manga. When he was offered the job the second time, he pitched the idea of using rotoscope. He thought if it was to be adapted at all, it should be done as a live drama. So there would be no point in simply presenting it in animated form, at that rate you might as well just read the manga and be done with it.
He says that he believes that when the mangaka draws this story he's seeing something 'else' which he expresses as a manga. At first Nagahama (the director) refused the offer to direct the adaptation, because he thought that simply turning this manga into a pretty, clean-looking anime would be pointless. In short (note that this is a quick & dirty summary):
