I think there could be a lot of meta-physical reasons for SG to beat Mary in FC but the real answer is that Grant Morrison really liked Supergirl (he said as much in interviews leading up to the fight) and wanted to see her beat a female hero of equal power (and who else outside of Miss Martian and WW are there at that level?). I also think that Black Mary/Evil Mary in Countdown was largely a result of Grant telling DC he wanted to use an Evil Mary Marvel in FC without telling them how she was supposed to get that way. So the Countdown writers (i.e. Paul Dini) basically made it up. Notice how Mary’s totally aware “deal with Darkseid” for more power at the end of Countdown does not at all jell with Morrison’s Completely Possessed Mary in Final Crisis. As for the JSA arc I think there was a LOT of Editorial influence there. It was co-written by Geoff (outside of Gail Simone the biggest Marvel booster at DC) and Jerry Ordway (who created the Post-Crisis version of the Marvel Family in Power of Shazam and was also the first comics pro to go on the record about his displeasure on DC’s “Evil Mary” in a web interview during Countdown) and it seems very rushed. At a post on the DC Message Boards Ordway said there were a lot of last minute changes to the story including the fact that Freddy had originally been in the story and the Wizard Shazam had originally not been revived. Also Alex Ross’ JSA cover has Mary in her “Black Mary” countdown outfit while Ordway drew the pink pony-tailed DeSaad Mary outfit within the book itself. It also doesn’t jell with any timeline since Mary said at the end of FC that she would never say the “Word” again and here she is right from the beginning of the story in league with Isis and Black Adam (who said he had regretted giving her power in Countdown and Final Crisis). Based on the non-resolved cliffhanger at the end of the arc, I tend to think that Johns and Ordway were basically told they had 3 issues to press the re-set button on the Marvel Family – Shazam’s alive, Freddy’s powers come from an entirely different source, Billy’s no longer the gray-haired Wizard, Isis is back and both Billy and Mary are de-powered. Unfortunately Mary paid the price again for Editorial decisions even by writers who liked her (I really think a huge part of what happened in Countdown and to an extent with Giffen and the Superbuddies is that the writers had no love or even liking for the character and it showed).