I always saw Alistair as a dark character since Origins. The guy was basically unwanted - his own father gave him away (although he doesn't know the reason why Maric gave him away), Isolde feared him and Eamon sent him to the stables then later to the Chantry to appease Isolde.
He joins the Grey Wardens and find a family there only to have them die at the beginning of Origins. That kind of thing does play a major part in Alistair and he does show how bloodthirsty he is when it comes to Loghain. He wants Loghain's head. He keeps it to himself but there is a reason why you cannot stop him from killing Loghain if he is the one to duel him.
Add in meeting his sister and having her tell him what she did (that his father forced himself on 'their' mother and that the woman died giving birth to him and his sister wanting nothing to do with him (except gold)).
Yeah - you have the option to harden or not harden him but I always saw that the events has already been taking their toll on him.
Then you remember that Alistair has always been wary of Morrigan joining the group - he even says that he thinks there is another reason why she joins (and he was right - she gives you the option to survive the Archdemon - by getting her pregnant - which could be a blow for Alistair if he is a romance with a female Warden and she asks him to do the ritual with Morrigan - a woman he doesn't like).
Then you have the whole thing about Morrigan asking you to kill Flemeth because she takes over her daughter's body. Flemeth offers you another way - to lie to Morrigan about killing her because she wants to see what Morrigan will do with her freedom. Sure, Alistair agrees (and approves) yet this just causes more distrust in wild witches in his part.
Everything with them seem to have a personal motive behind it.
Killing Yavana - I got the impression he was just tired of everything that was going on. Yavana says Maric was supposed to come back to help her awaken the Dragons yet he did not. She offered to help Alistair find his father - IF he awakens the old Dragons. To Alistair - it seems like everything needs to be a ritual and he is just tired of it.
He even says that Morrigan, Flemeth and Yavana lies and manipulate everything. Yavana says it this their craft - yet not their purpose. At this point - what reason does Alistair have to trust Yavana in anything she says? Flemeth disappeared (yet he probably heard how she helped Hawke - since Isabela and Varric are part of his party). Morrigan disappears after the final battle with a child (if the Dark Ritual was taken) or she left before the final battle because her ritual was not taken - leaving them without added support (which could embitter him further to her).
Considering Flemeth's words in Inquisition - I think he has a good reason to worry when it comes to the witches (and his blood). (and Grey Warden!Alistair says he met his father in the Fade so I guess we can consider he went through the same situations in the comic as King!Alistair).
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For Leliana - she was always dark. Even after killing Majorie - she admits that she liked killing her, that she likes playing the game and admits that scares her. You have the option to tell her to embrace it or to know that it is not her. Either way - Leliana pretty much goes to work for the Divine, which takes her away from the Warden (who could have been a good support) and ends up using her abilities to help the Divine as the Left Hand by murdering, blackmailing and getting secrets.
She is a spymaster for a reason. I think the loss of the Divine (and her shaken faith in the Maker) has made her steel herself. With the Warden disappearing (who could be considered as the only person she trusts), she probably fears the worse and does not want to feel that again which is why she says to kill the traitor instead of making them work for her.
After everything they had been through - it is not really a surprise that they fell into the darker aspects of their lives.