I basically considered this to be a continuation of the cycle.
It could just be that I crossed over a threshold with regards to how much Morrigan liked my PC when I killed Flemeth, but afterwards her dialogue was slightly different. Not just more friendly, but how she was speaking was subtly different. Additionally, the robes you get are the 'robes of possession', so I am thinking that Flemeth takes over Morrigan either through the robes or upon her death. Not to mention the fact that Morrigan thinks that Flemeth will be back in some form or other - perhaps a subtle hint that she knows she is...
Another thing that makes me think this is how surprised and somewhat annoyed Morrigan is that Flemeth makes her go with the party, yet right at the end has some remarkable insight as to why she wanted her to go - a set of variables in place that is a remarkable coincidence unless she had prior knowledge - i.e. Morrigan is Flemeth.
I think the idea of 'softening' Morrigan as a male PC with romancing her probably helps, but obviously, they don't want to give too much away with regards to possible extensions to the franchise. I'm just happy that her being upset about the whole having-to-leave thing is reflected in the voice acting if the romance does happen (can't say first hand since I haven't romanced Morrigan as yet).
Its an interesting conundrum, no doubt. But I think letting Morrigan 'have her way' will make for much more interesting gameplay later on.