User blog comment:FTWinchester/My Problems on Naomi's Character/@comment-108.16.120.27-20130518022439

In the show it was revealed that Naomi worked as the head of the "Intelligence" arm of Heaven as such it would place her under the direct command of the Archangels which their mission to gather intel and make sure that the angels are kept in line if they weren't they were to be executed. As well during the Civil War she was most likely either neutral in the affair or on the side of Raphael along with her faction so probably didn't let him win, she just kept to the shadows has she had done for thousands of years before revealing herself between Castiel's disappearance and Hester's death.