You don't have to be a Catholic or Christian to love a beautiful Cathedral/Church. It's' architectural heritage, not religious heritage. And Vienna is not a religious city what so ever.

Putting al the museums all at the same grounds is a bad idea. The district will be overloaded during peak tourist hours and dead out of opening hours. Businesses like restaurants or bars will have a difficult time, only having a limited time window where customers are around. Other neighborhoods where a museum could be a useful addition are lacking one, since there can only be so many museums in a city of a given size.