Flemeth is complex. When Morrigan told me about the Black Grimoire and bid me kill her, I was suspect. Literally, up until that time, I actually liked Flemeth (from the Warden's POV), up until that moment, she did nothing but help you. She protected the treaties, she save the Warden at the Tower, and she gives you a hawt mage to take with you.
On some playthroughs, I killed Flemeth, on others she and I came to an understandng. Despite the sinister conotation, it seems that there isn't much difference which way you choose, kill her, she still lives, don't kill her, and nothing much changes in the timeline. The only unaddressed issue there is if you didn't kill her.... and Hawke delivers the amulet... there are techincally 2 of her out there.
And yet, if you romance Morrigan, you see, at the very least, what a stern and intolerant mother she had been. Until the Warden, she had never had a friend, and was taught friendship and love are weaknesses. Of devouring chasin men of their souls. In DAO, in the Fade, when loving Flemeth is exposed and strikes Morrigan, (Morri) reacts that that is more like the real Flemeth, so there is clearly physical abuse in their history.
In the end, Flemeth seems like both an effective mother (making her daughter strong and able to deal with the evils of the world) and yet, both an abusive, manipulative and cunning harpe in waiting. Yvanna claims is that Flemeth's possession is a gift, calling Morrigan a confused child, it lends credence to the idea that a soul is not forced on another, and yet, who knows how manipulated Yvanna has been by Flemeth. Still, it seems that Flemeth has her eyes on Morrigan over Yavanna for something big... Not sure what the end result was supposed to be, but I feel that Flemeth severly laments the HoF's... Bad Influence on Morrigan. She probably laments saving the HoF and Alistair at the Battle of Ostagar.... if given a second chance, she probably would have save Duncan and a few other GW. Either way, Flemeth is a shitty mother.