The Paris court ruled that Onana's writings violated France's laws prohibiting genocide denial and incitement to hatred, noting that France would "no longer be a haven for denialists".
Prof Muganga drew from his past experience as a Munyarwanda in Uganda and spoke of how his family narrowly avoided expulsion in Masaka for being Banyarwanda.
Rashid Hakuzimana, who was arrested in 2021, denied all the charges, which also included inciting ethnic division and spreading false information for claiming that anyone who dares to challenge President Paul Kagame in elections is jailed.
Charles Onana, 60, author of "Rwanda: The Truth about Operation Turquoise" published in 2019, faces charges of denial and minimising of the Rwanda genocide.
Marburg, a highly infectious hemorrhagic fever, is closely related to the Ebola virus and is transmitted through direct contact with blood and bodily fluids.
In a statement, the Ministry of Local goverment said the suspension of the faith-based organisations follows an inspection exercise to assess the compliance.