A number of things set Perra's efforts to clear Redcliffe Castle apart from all the other playthroughs I've done before. First of all, she chose the Templars over the Mage's Circle and effect of this action is seen before the Castle stage is through. Second of all, Perra has chosen to include Alistair in the fight. For some reason all other characters (completed stories and false starts combined) have left Alistair in camp in favor of Zevran, Sten, or Shale. It is a little unclear why this has happened since enlisting Alistair to help liberate his childhood home makes a lot of sense when you think about it. His presence does not seem to make a whole lot of difference one way or another, but his comments in game make it clear that he is a conflicted man.
After Defending the Village - Our hero and her partners in crime met up with Bann Teagan as promised. They learn that there is some kind of demonic force resurrecting the dead inside the castle (surprise!) but the Arlessa is all kinds of vague about how it really came about. I fact she also falsely accuses a mage of calling it into being.
Enter the Mage - The first major decision of this stage comes soon after Perra enters the castle through its dungeon. Here she meets Jowan, a blood mage imprisoned and tortured by the arlessa and her men for something they know he didn't do. Granted, Jowan is no saint. He may not have brought forth the demon, but he is guilty of poisoning the arl at Logain's request - an action that sets up the demon calling. Perra has four options - killing him off the bat, leaving him to rot in his cell, letting him run away, or letting him out of the cell so that he can make himself useful and ultimately redeem himself. As with all the other characters I've played, Perra chose the last option - giving him a chance to redeem himself.
As a Circle mage, one of my characters granted him this option because of their former friendship. As a human noble my character recognized his special abilities (blood magic) and knew that they may need him to cleanse the castle and ultimately restore order within the arl's home. As a city elf I let him free for no real reason since it was my first character and I was still figuring out the lore. Were I to play a city elf again I probably would have let Jowan run since the city elf has no love for human nobles and likely would have some kind of affinity for apostates. As a Dalish elf I never got this far.
For Perra this was a matter of redemption. She has no particular love for mages, but she knows what it is like to find oneself trapped in a bad situation with no way out. By letting Jowan help she knows that he will eventually have to submit to human authority and pay for his crimes (as he should) but at least he may have a chance to reverse the situation and clear his conscience. He at least deserves that much. Alistair (the Templar) did not approve of this decision but it netted approval from Morrigan and Leliana.
Enter the Child - After fighting their way through legions of the undead, Perra and her companions come face to face with the demon ... a demon who quasi-possesses the arl's only son Connor. It appears that the arlessa knew all along that it was her son and not Jowan who had called forth the demon (I mean Connor was the only abomination in the room) but at this point she is so far in denial that she has almost convinced herself it was all Jowan's fault. As she so aptly points out, Jowan set up the situation (poisoning the arl) that paved the way for Connor's connection to the demon (the being baited Connor with promises of the arl's continued life). It is not until Bann Teagan calls her on it that the arlessa recognizes her role in it all - she was the one who employed an apostate to help Conner hide his latent magehood.
Jowan presents Perra with one option - allow him to sacrifice someone so that he can use their blood and enable another mage to enter the Fade. In the Fade this mage could kill the demon and spare Connor's life. The arlessa offers to sacrifice her life in exchange for her son's. The other option is to simply kill Connor. By killing the child Perra would sever the demon's connection to this world and end it all.
Consequences of Perra's Actions - A third option is made unavailable due to Perra's decision to cleanse the Circle. With the Circle's help she would have been able to send a mage into the fade, slaughter the demon, and save Connor's life without another's blood needing to be spilt. Siding with the Templars, however, means that in order to terminate the demon someone had to die - the arlessa or Connor.
The Child Must Die - Perra chose to confront the demon on the physical plain. It is true that none of this would have happened without the arlessa's interference, but at this stage in the game there is no guarantee that Arl Eamon will recover from his poison induced coma. Everyone has set their hopes on the mythical Urn of Andraste's Ashes, yet even if the Ashes actually exist there is no guarantee that they actually possess magical healing powers. Thus by allowing the arlessa to sacrifice herself, Perra might be depriving Redcliffe of a ruler. The arl might not recover, Connor would eventually be sent to the Circle no matter what because of his connection to the Fade, and it is likely Bann Teagan has other responsibilities besides taking care of his brother's land. The whole reason that Perra is at Redcliffe in the first place is because of the need for assistance with the Blight. Removing the arlessa means that Perra might be losing the military and political assistance form Redcliffe that she so vitally needs. In addition, Connor has already been possessed once by a demon. There is no assurance that if severed this previous connection will not make it easier for him to be possessed again. It is better to nip the problem in the bud and be done with it. The arlessa pleads with Perra woman to woman, but Perra is not making her decision personal. For the first time she is putting all else aside and making her decision as a Grey Warden.
Alistair's Rage - Alistair is a very conflicted man. While in the castle he clearly states that invoking blood magic to kill the desire demon simply piles one sin on top of another. Two wrongs don't make a right. Back at camp, however, he rages at Perra for killing Connor and claims that she should have let the arlessa sacrifice herself. (Previous walkthoughs tell me that an angry confrontation would have still happened if Perra had chosen to use blood magic.) It seems that Alistair, like Perra, has a number of issues reconciling his personal past, his past with the Templars, and his duties as a Grey Warden. As a Grey Warden both possible choices were reprehensible, but I'm rather certain that blood magic has historically been allowed by the wardens as a means to an end. As a Templar there was no excuse whatsoever to encourage blood magic, and as a human being Alistair was devastated by destroying the arl's only child. How on earth can he face Eamon now?
While frustrating game wise since in Perra's scenario there was no way to win with Alistair, it is his indecision that makes the character so very human. There is nothing even remotely positive about sacrificing the arlessa or killing a little boy and I think that Alistair is DA:O's way of reminding the player that just because something helps achieve the ultimate goal doesn't mean that the decision is morally correct. You always have a choice. In this case they were both bad choices, but you always have a choice. Alistair's moral barometer is the game's way of making sure that Perra, and my other heroes, don't forget the emotional/personal consequences of sacrificing one being for the sake of the greater good.