Wouldn't that make The Warden's actions pointless in attacking and killing Flemeth (until Hawke brought to life a portion of Flemeth's essence) to give Morrigan enough of a reprieve to make certain she would be safe (assuming the player made that choice, and didn't betray Morrigan's trust by deceiving her)? If The Warden chose Morrigan, I'd prefer to see Morrigan and Flemeth as two separate people.
Yeah, it seems like that would totally undermine the whole Grimoire/kill Flemeth quest from Origins. The entire point of that was to buy Morrigan some time. I don't see when Flemeth would have had the chance to "possess" Morrigan's body. I don't remember exactly how many years passed, but there was a while there where Flemeth was out of commission, she was reliant upon Hawke bring her back to life, and Morrigan was beyond the Fade with the OGB.
I suppose anything is possible ... just seems very unlikely. Mike Laidlaw and the writers said that Inquisition is "Morrigan's moment," not Flemigan's moment.
Honestly, I think the only reason that rumor got started was because Morrigan looks slightly different in the 2013 E3 trailer than she did in Origins, but that is to be expected given that this is an entirely new graphcis engine and an entirely new character model. One beauty mark and we are automatically supposed to assume that she is possessed. Yeesh.