Yes originally I hated Mary's role in FC but after re-reading the only problem I had with it is Supergirl getting the upper hand on a fully-powered Mary at the end (WW I could understand but Supergirl?). Morrison does make it pretty clear that Mary is possessed by DeSaad (although it takes everybody but Black Adam forever to figure it out) and pretty much ignores everything that went down in Countdown (as most writers have since). Still when you add Final Crisis along with Countdown and then the JSA arc where she went evil for the 3rd time - it just seems like too much for no reason and she didn't have a chance for her to act heroic at all at any point.
Do agree with Sterling Gates though. This is how I wish Kara had been written from the beginning. She's a young girl with a good heart that cares about people, not a moody, hostile anti-social mess.