Sialater wrote...
OK... but about what? At that point that "bargain" hasn't even been broached.
The
"Yes she does, the question is, do you?" comment which is registered as her knowing Morrigan has lied to the PC, is all to do with how Flemeth extends her unnatural life, Flemeth knows that Morrigan has told you the 'tale' that Morrigan said regarding bodyswapping. She knows this because she has also told it herself.
Out of the two of them, Flemeth tells more truths than Morrigan does. Not only that she has really good foresight, because (if you've read the books) she told Maric that Loghain would betray him again and again each time getting worse. I believe that when she tells the PC in the first encounter that the wardens face a greater threat behind the Blight, she wasn't referring to the Archdemon, think about it, every Blight has one of those, I believe she was in fact referring to Loghain screwing things up. She also stated that Ser Jory was sadly not important in the grand scheme of things, I think she knew he didn't have the courage to go through the joining and thus knew what the outcome would be.
The thing is, a lot of people (and even animals) tell lies, to some it is a 'survival' tactic and it generally works well for them. As has been stated Morrigan just as much as Flemeth considers survival a big thing. That doesn't make them
evil as some people claim them to be. If they were evil and wanted that old-god baby as bad as people believe then they would have done the ritual by force. Instead she walks off, not too happy but without any undue fuss. Just means they possibly have to wait another few hundred years to try getting that power again or seek some other means of power (become a member of the royals in Orlais.. perhaps

)
To go back to the OP topic header, considering that David Gaider has stated that if they do a sequel then there will be a canon ending, then it would seem a bit strange that they did make it optional if it is supposed to have happened according to the canon, but if it wasn't then in some respects the refusal of it does play a part in the canon as well potentially.
They can get round the origin of the Warden simply by just referring to him as "The other warden". Which makes me think though that if they go with the non-ritual ending then it will be either Alastair or Loghain that made the sacrifice with 'The other warden' going off into the deep roads.