This part seems quite fine to me ...
As you said, Morrigan was just paranoid "again" ... so at least if fits her character.
What pissed me off was when i find out in Inquisition that all important choices you made, were negated.

Killed Flemeth? > Nah, alive again.
(Ok, we were told that we will most likely not actualy kill her ... since she is too powerfull to that ... so i would probably be willing to forget this.)
Killed Morrigan? > Nah, alive again.
(Even tho we never actualy seen her corpse ... so this one could be also forgiveable.)
Killed Leiliana? > Nah, alive again ... even remembering her death.
(Dunno if someone thought that would feel better for players, like their action indeed actualy happened ... but it semed like spit in the face to me.)
But this particular death i just cant forgive ... there must have ben sooooooooo little people in the world who actualy did what you need to do in order to kill Leiliana ... (even tho i never understanded what people like about her, she seems pretty anoying to me) first and foremost i just dont understand
why it was so important to bring
*her* back?
No other person in whole Thedas was fit to become spymaster??? O_o
I can totally get that Flemeth was ancient spirit, and Morrigan super special witch with very rare training and lots of specific experience ... but what makes Leiliana irreplaceable?
She just stands next to the table, frown and try to look cool. O_o