A third person is to be made redundant and will go soon, leaving nine staff led by Les Hems, the organisation's development director, and Tom Lasparini, its operations director.
The news comes as GuideStar's current funding runs out this month and it seeks more commercial contracts to secure its future.
Hems said the departures were "part of the natural progression of the organisation from the implementation to the operating mode".
Roberts was unavailable for comment but has told friends she is "moving on to set up an initiative linked to the 2012 Olympics".
Hems said he was confident GuideStar could continue to be independent.
Efforts to secure new business had brought "signed agreements in single figures and negotiations in double figures".
Modelled on a US website, GuideStar was developed with a £2.7m grant from the Treasury and £1.9m from other sources. Its searchable database takes data from the Charity Commission and allows charities to add information about themselves.
Hems said GuideStar was not looking for new grants but was trying to secure contracts to provide data to government departments.
- See Editorial, page 22.