Would Julian's 'Pagan Church' have been any different from the Catholic Church.?

I have read that the Neo-platonic Emperor, Flavius Claudius Juli, attempted to institute a pagan church on the christian model, with the Transcendent One taking the place of the christian god, and the other gods such as Mars and Venus taking the place of the angels and saints. The problem is that this system is exactly why the Catholic church is so distasteful to me. It was due to this model that the crusades and inquisitions happened. Would the middle ages have been any different, religious-wise? If my information is faulty, please provide sources to the contrary.