My understanding is that he just resigned his Kancho title which is different from resigning from the organization.
the "Kancho" title is the important one. The Kancho is the head of the style. He sets out the direction of the style from a technical perspective.
"Soke" is a political, figurehead position. Gozo Shioda's eldest son, who does not do aikido, was Soke for a period of time.