The board of Common Weal said Robin McAlpine would step down from his role with immediate effect and take on a new role within the organisation focusing on policy development.
Mr McAlpine had written an article on Common Weal’s news analysis website Source alleging Ms Sturgeon had “developed and executed in secret” a “coordinated plan of action” to drive Mr Salmond out of politics.
He also compared the First Minister’s handling of the Salmond affair to Richard Nixon and the Watergate scandal.
An inquiry into the Scottish Government’s handling of harassment complaints against Mr Salmond is underway and Mr Salmond was acquitted of sexual offence charges during a trial last year.
The piece received a hostile response from many on social media and was denounced as a conspiracy theory and misogynistic.
In the statement, Common Weal announced an internal restructure and “audit” of internal systems”.
They said: “The Board of Common Weal and the Director, Robin McAlpine, believe nothing must be allowed to distract from the important work of the organisation. Our policy platform and campaigns have become central to the case for a progressive independent Scotland and are available to all who support this cause. This resource is more vital now than ever.
“A recent article written by the Common Weal Director, and its fallout, has threatened to disrupt the common purpose of the Common Weal family as we pursue this goal. As a result, Robin has asked to step down from his position as Common Weal Director. He will focus on a new role dedicated to policy development while a new director will lead the whole team.”