You restored a tainted god to an untainted god soul. People assume she is going to use it for power or evil but I just don't really see it that way. I feel like she's not really done anything that is evil and is working slowly toward doing what she can to help the world in her own way. When you go for the grimoire, she offers to just give it to you if you leave her in peace. Now this is particularly telling because you can kill her but she won't die. She knows she won't. She made plans. Several from the sounds of it in DA2. So she pretty much knows she will survive though not 100% certain - more like 99%. But still she doesn't really want to fight you. I don't see her as evil. I see her as willing to exact justice on people who have done bad things that have harmed others. I think she also wants to preserve what she can by saving the old god from the taint or death. The assumption was actually that morrigan would use the child as a source of power but morrigan turned out to love him more than most could have imagined.
It surprised me. Morrigan at the well was 'same old power hungry Morrigan', but the whole "you will be bound to Mythal" definitely put off my Dalish mage (who was wiser than Morrigan in the ways of such things it would seem), so I let her drink it, not knowing what would happen really.
Then the following scene with Flemeth in the Fade made me cry. To see Morrigan, the same power hungry Morrigan from Origins, admit in one breath that yes, she had planned to use her son, initially, but then grew to love him and then beg on bent knee for Flemeth to take her instead of Kieran made me cry. There were hints earlier where she talked about how she wouldn't raise him isolated from the rest of the world in a swamp (or something along those lines) made me realize that Alistair's son wasn't going to have a bad life, even if now he's just a normal little boy.
And Flemeth looked so sad, like Morrigan had cut her to the quick.
Morrigan's heart was finally touched by her son and she learned compassion.
I also liked the grey warden symbol on his shirt--a homage to the HoF, who is a friend or may also be potentially the father, I am certain.
In all it's one of the most powerful scenes in the game and one of my favorites.