The organization is taking these claims extremely seriously and cooperating with the police. Fawcett has already stepped down, and the royal family have severed ties with him. Prince Charles had nothing to do with the scandal; although president of the foundation, he's not involved with its day-to-day governance.
Prince Charles may claim to have been kept in the dark, but Mahfouz was awarded a CBE at Buckingham palace following massive donations to people with links to the prince, and there's even a forest named after him at one of the prince's residences. Clearly this is a case of scandal and corruption.
Regardless of whether or not Prince Charles was directly implicated, these revelations will only act to deepen the crises currently being faced by the British monarchy.