I've seen different opinion on that. Some wanted her dead, other thought it was fair enough.
I personally liked Freya a lot, probably one of the most complex and well written characters. So to me the punishment that she would get in the end does not really matter, as long as it was consistent with everything else.
If she was sent back to heaven, we don't know what would happen to all the high level adventurers of her Familia. So, I guess keeping her around was just to also keep them around as Orario will need them later on. It was the most logical choice.