Flemeth was going to inhabit her daughters body as she had done many times before, the mother, just like the daughter, heartless/ cruel. You see, if you picked up from her dialogue from the very beginning it seems Flemeth (Morrigan's mother) was setting Morrigan up to be the body she inhabited, she was sending her out to strengthen that body through experience. I've come to the conclusion that Morrigan is selfish and actually quite heartless and yes. I just played through DAO for the fourth time now just to look at it from every angle. sequel hint? I think it would be the best canon ending. I don't know about you guys, but at the end of my uh, ending, it says "but that was not all that the land of Ferelden heard from the Grey Warden". So I actually think I got the perfect ending, where pretty much everything good happens (Alistair and Queen whatshername rule together and unite the people, the one chick rules the elves who are now curse free, Bhelin expands rights for dwarven castless, no Grey Wardens die fighting the Archdemon, the ashes of Andraste are saf- oops wait, forgot to go back and kill the High Dragon! Oh well) and there is a little bit of mystery in the child. She can't totally disappear, especially with the special connection ring, so maybe you can find her later and make sure she's not effing up your kid.
You can also tell Morrigan that you vow to find her afterwards, and also say the same thing to Alistair when he asks you what you plan to do after you kill the Archdemon. Templars are kind of dicks anyway- they should be hunting down maleficars only, not putting every mage they can find through a test where they kill you if you don't pass. Personally, I think she wants to use an Old God's power to destroy the Chantry, which I don't consider an evil thing.
However, I think there may be a clue when it says that she goes to Orlais, because Orlais is the home of the Chantry, which she naturally hates as they impose on people's freedoms (specifically mages). She obviously wants to use it for something, though, and nobody knows exactly what. This implies that she won't teach it to hate and kill everything, which doesn't seem to be Morrigan's desire either.
If you ask her how she will raise the child, she also says that she will teach it to "respect where it came from" and that it will be free of the taint that creates Archdemons. but if, at that point in the game, you threaten to use the anvil on her, she says something to the effect of "point taken" and backs down (I think she gives -1 disapproval or something).
So when she does things like advocate the use of the Anvil in Orzammar, she only sees the benefit and doesn't consider how it would feel to have someone force you into being a rock monster. I mean, she was raised in the woods where she was forbidden to come into contact with people because it could lead to her discovery as an unsanctioned mage. But in the end, I decided to accept her offer because her dialogue throughout the game convinced me that she wasn't truly evil, just completely lacking empathy. The Morrigan thing threw me off too, because I was also playing a nice guy who was romantically involved with her (I was determined to get my Warden some action and it was either her or Leliana, and Leliana was just too goody-two-shoes even for my character).