I think people are overstating this "change" in Morrigan. While the dialogue doesn't let you fully investigate things properly she does know that the Well involves personal loss but you can only ask about that if something happens to her and what it means for her son, rather than asking the more obvious question of that drinking from the well could cause her son to be in danger. Despite this risk she still lusts after the desire for power so much that she can kill Abelas for the opportunity. Just like in DAO she joins the group under the premise of saving the world but still has hidden motives in doing so in her quest for more power. Yeah she gets all emotional with that whole Fade Flemeth stuff but she still is after power. The only really difference is she cut out the scathing sarcasm. She is still the same is most respects.
When it comes to Leliana it boils down to who you really think she is. While some people think the darker version is her true self I think it's actually the opposite; the dark version is somewhat of facade she puts on for her job and gets a bit corrupted by it-she just gets really invested in it and starts to really affect her real nicer self and leads to internal conflicts. Meanwhile off the job she has been shown to be the nicer "unhardened" character that seems to be her "true" self. In her DLC she is more fun, willing to do almost anything for the person she loves but shows morals and concerns about the plan. In Origins she speaks up against spoiling the Ashes and if she leaves via disapproval it's because you do "evil" things. As Hand, Leliana has to reprise her bard role; she can recognize strengths and weaknesses and since she is protecting a woman and institution she loves and will go to any lengths to fulfill that defense which is kind of like a warden do anything for the job. In DAI it's pretty much the same thing but with the added pressure of Justinia's death baring down on her. In these situations when she's on the job not only is she going through personal issues like recalling the pain from Marjolaine and the death of Justinia but she is surrounded by 3 of the most powerful people in Thedas with decisions that shape nations. She needs to be more ruthless to get the job done and will adapt to the needs and influence of the PC. She gets overly invested in her work causing her to become darker as her concious is dealing with all these problems; Blackwall says something like "She seems lonely all she has is her work." Even with this darker persona you still see the nicer side in some of her war table banter and quest solutions. Similarly Cole sweetening her wine to help her suggests she is having issues with what she's doing.
When you look at her response to Justinia's message you recognize that she thinks Leliana is a "good" person. The letter from the romanced Warden is pretty much the same thing. Josie mentions that she used to sing in halls and be graceful and cheerful before this whole Hand business started. These are the people who know her best and all have the same conclusion that she is a nicer person. And after you beat the game and return to Skyhold she has big smile and is nice and friendly even if hardened. This seems to be the "real" her as she can lay down her burdens and doesn't have duty interfering with who she is. When she is on the job she becomes darker (such as a hardened Divine ending) and driven when off the job she is certainly no angel but has always been shown as kinder and gentler without having the burden of saving the world and the necessary attitude for that.