I think some things changed between Witch Hunt and DAI/trespasser.
In Witch Hunt Morrigan implies she knew what Flemeth was ..."she's no blood mage , abomination , etc...she's not even truly human."
Thing is...technically speaking Flemeth was still human and was an abomination.Sure she didn't get posessed by a random demon or spirits ...
Besides she's horrified when she tell you this , in DAI she tells you "I suspected she wasn't truly human " well girlfriend you certainly were very dramatic about a couple of suspicions.
Then she says Flemeth isn't craving immortality and she was wrong oh so very wrong.In DAI she's still at square one claiming Flemeth only wants to posess her to prolong her lifespan...So Morrigan what about that terrible plan you knew about?The one not about immortality , well it seems you forgot about it.
Finally she tells you Flemeth is linked to the Blight and as a grey warden you should hunt her ASAP.Again in DAI no one talks about Flemeth and the Blight.Morrigan isn't accusing her of anything Blight related.
Then Morrigan claims change is coming to the world , and it would set people "free" , well yeah?...I think she was talking of the veil getting destroyed there .But again in DAI she has no clue what's going on , she doesn't even know what she's doing with Kieran except the OGB has some unclear destiny.
So I think a lot of things changed , someone wanted to tear the veil down from day 1.I doubt it was supposed to kill everyone though , just bring "change" .Like Sandal prophecy , there's no "this world will burn in raw chaos " nah it was everyone will be as they used to.
If I had to guess after ME3 synthesis ending I think the devs figured out the whole green energy turning everyone the same and equal (immortal/magic) was going to horrify some people.So now tearing down the veil is kinda bad , and Fen Harel is an antagonist.