[1] https://en.m.wikipedia.org/wiki/1905_French_law_on_the_Separ...
I made a bit of research, and while the sources are somewhat contradictory - the article linked as a source by Wikipedia contradicts what is stated on Wikipedia! - my understanding is that you are correct: - nationalized in 1789 - the Concordat (Napoleon, 1801) confirms the state ownership, and usage is granted to the Church - a few laws in the 19th century states the state pays for the maintenance of the building - law in 1905 confirms (again) state ownership, usage assigned to the Church
Also, the Catholic Church is a 2000 years old organization. There’s a lot more to it than the sex abuse scandals.
If it makes you feel any better the funds are probably going to come largely/entirely from private charity and the people behind know rebuilding notre dame makes fine business sense even if you have no sympathy for the church.