Yes, they did.

The main source for these claims is Jacques Tronchon's book L'insurrection Malgache de 1947 (the Malagasy Uprising of 1947). This book came out of Father Tronchon's doctoral work at the University of Paris in the early 1970s, and was updated and re-released in 1986 for the upcoming 40th anniversary of the uprising. In producing that work, Tronchon relied on interviews with over 150 individuals who experienced the uprising, as well as consulting restricted archives in France.

In that work, Tronchon estimated that violence surrounding the uprising and French suppression resulted in the deaths of approximately 90,000 people. An article by Le Monde Diplomatique from 1997, the 50th anniversary of the uprising, quotes Tronchons number while going on to cite other estimates which estimate deaths over 100,000 people.

However, Omar Garcia-Ponce and Leonard Wantchekon provide a survey of recent scholarship and mention a range of estimates for deaths:

While there is no consensus on the exact number of the casualties accrued during the uprising, all reported figures are indicative of a brutal massacre. French authorities originally alleged only between 8,000 and 10,000 casualties, a number that is now proven to be far from accurate. Depending on the source, reliable estimates range from 30,000 to 100,000 deaths. For instance, Jacques Tronchon (1986) talks about 80,000 victims, while Lucile Rabearimananam (1997) suggests that at least 60,000 persons were killed. A more recent study by the historian Jean Fremigacci estimates between 30,000 and 40,000 deaths, of which 10,000 were due to violent death, and the rest caused by disease and malnutrition (Fremigacci 2007).

Meanwhile, Jean Cole summarizes the uprising and repression thusly:

According to written historical accounts, fighting erupted simultaneously at a number of points on the east coast on March 29, 1947. Rebel bands that were drawn from the ranks of the hungry, dispossessed peasantry but were often led by former soldiers who had fought for France in World War II attacked military garrisons, administrative centers, and Malagasy sympathizers with the colonial regime, burning buildings and killing a number of French administrators and settlers. The French colonial administration responded with force, leading a campaign of military repression whose savagery was matched by the brutality of rebel soldiers who often forced civilians to join their cause. The rebels, who had sworn oaths to save their ancestral land or die, fought on. As the French army slaughtered cattle and burned towns and fields in retribution, rebels and civilians alike found themselves without food. Hampered by inferior weapons and weakened by hunger, they were beaten into a slow retreat. The historian Jacques Tronchon (1986) estimated that by the time the rebellion was declared officially over in December of 1948, 550 French were dead, and 100,000 Malagasy had been executed, tortured, starved, or driven into the forest. Over 11,000 appear to have been killed as the direct result of French military action. Though one recent historical analysis has contested the number of people who died (Fremigacci 1999), the rebellion remains a foundational event in contemporary Malagasy history.

Thus, she seems to be taking Tronchon's number, but saying 100,000 Malagasy suffered atrocities, but only 11,00 were killed by military action.

The specific claims and wording of the Wikipedia article appear to closely follow Felix Schuermann's entry for Madagascar in Sage Encylopedia of War which says on page 1004:

France Crushed the uprising with sheer brutality. Under General Pierre Garbay, French forces pursed a strategy of terror that involved aerial bombings of alleged rebel strongholds, burning of villages, machine-gun mass executions, torture of prisoners, war rape, and "death flights' -the throwing of live prisoners out of airplanes.