Crown prosecutor Lance Rowe said no evidence would be presented for the remaining charges.
McGregor was given interim name suppression at his first court appearance on July 17, 2012, however Justice Young yesterday ordered it lifted.
The hearing was meant to take place using an audio-visual link however technical difficulties meant that a telephone had to be used.
After McGregor made his first court appearance last year, the officer in charge of the case, Detective Senior Sergeant Neil Forlong said up to 20 staff worked on the case and medical information that recently came to hand resulted in the arrest.
Hinekawa's death resulted in numerous editorials in various media and made Paula Bennett, Minister for Social Development, visit Wanganui after originally having declined an invitation to a community meeting in the city regarding her Green Paper for Vulnerable Children.
Former All Black Norm Hewitt, who fronted a campaign against child abuse, said at the time Hinekawa's death was "like the shock of a 7.8 earthquake".
McGregor had initially pleaded not guilty and was to face a jury trial next month, set down for four weeks.
He was remanded on electronic bail until October 29 when he is to present himself at the Wanganui police station to be held in custody until sentencing on December 18.
Justice Young also ordered a pre-sentence report to be completed before then and ordered an agreed summary of facts be filed for media.