A French court found Bob Denard, nick-named the Pirate of the Republic and now suffering from Alzheimer's disease, guilty for his role in the 1995 ousting of Said Mohamed Djohar, then president, and gave him a five-year suspended sentence.
Idriss Mohamed, a political prisoner for four years under a Denard-backed government, said on Wednesday: "I'm completely outraged by this sentence.
"Finally recognising his culpability, they then give him this symbolic penalty. A country which claims to defend human rights has shown its true face."
One of France's most notorious mercenaries, Denard had a violent career in the archipelago, stretching back to independence from France in 1975.
Denard's accomplices, also found guilty, were given suspended sentences or not penalised.
Denard's lawyer says the sentence reflects time passed since the coup and the fact it was bloodless.
Ali Mohamed, 35, said: "It's ridiculous. This isn't justice. They should have put him in jail for life.
"When Denard ran things, men were disappearing - the mercenaries killed people. I once woke up to find the bodies of two opposition members in a plastic bag on the street."
Denard's favourite target was the Comoros and he was responsible for much of the instability on the islands, which only in May had their first peaceful handover of power in three decades of independence.
Denard deposed the islands' first post-independence president, Ahmed Abdallah, in 1975, then restored him three years later in a second coup.
For the next 10 years, Denard ran a lucrative business empire under Abdallah.
But in two of Denard's previous coups, including one against Abdallah in 1989, the deposed leader was killed under mysterious circumstances, although Denard was acquitted of killing Abdallah by a French court in 1999.
The French army intervened a month after the September 1995 overthrow of Djohar, capturing Denard and his fellow soldiers-of-fortune and putting them on trial.
Denard served with the French marines in Indochina in the 1950s and then joined the French colonial police in Morocco.
In his high-profile career as a mercenary, he led ruthless, often ill-disciplined bands of former European soldiers, sometimes dubbed Les Affreux (The Terrible Ones) in wars in the Congo, Biafra and Yemen.