There's no way Azura could not have known of the consequences of destroying the Red Tower, and she personally oversaw it's destruction. Did she do this with the intent of fooling the Nerevarine into doing so in order for the Oblivion invasion to be possible, or did she guide the Nerevarine to do what had to be done in order to save Morrowind and ultimately all of Tamriel? Is it perhaps possible that she DIDN'T know about the consequences?