I have been in it. It is itself beautiful and the space it creates in the city is incredible. I want to reiterate that I believe a potentially different idea added to the existing building is probably impossible to achieve because the original is just too powerful of an idea and image to manipulate and reenvision. Having it be the roof only is a constraint that even the best design can not overcome.
In general though, I believe that it is ok to at least have a conversation about how a building can change for future generations. You're probably right in this case though and maybe the existing story of Notre Dame is in itself powerful enough to last another 500 years. What do you think it will it look like in 1000 years?