Stanises motivations remained consistent in my opinion. The Iron throne was always his goal, and still is. And burning people alive is nothing new in his camp. I think he (and Melisanre of course) sees the burnings as the necessary evil needed to reach his goal. It's desperate times like these (when he can't turn back, and probably won't succeed if he goes forward) when he needs all the help he can get in order to reach the goal. Thus the desperate measures.
Yeah, I can clearly see the "do anything necessary" theme that they've shown with the character in the show. I just wish that his book theme - duty above all else - would have made an appearance. His duty to his daughter and only living heir is more important to what I personally thought his character valued.
I know that Azor Ahai had to make sacrifices in the prophecy and Stannis himself has said that true sacrifices have to hurt, or else they're not true. This just seems spiteful and cruel, something Stannis is not. He's dry, dull, stern and consistent to a fault. For a man who wanted to earn the throne rather than just take it, the cruel death of his innocent daughter is not an act 'for the good of The Realm' and can never be perceived as such, unlike other controversial decisions (Renly, dick leeches, going to the Wall, burning the false idols).
I agree with Andrei Bisca: Stannis' motivations seem quite consistent. Throughout the show, until the start of this season, Stannis was always depicted as being someone that had no problems doing (necessary) evils (supposedly for the good of the realm) in order to reach the Iron Throne. This season however they showed you a more compassionate side of him, that of a father that dearly loves his daughter. They just wanted you to see how much she means to him, so that you'd know that in his mind he's making the greatest sacrifice he could ever give.
Rule of thumb with Game of Thrones: The more they make you care about a certain character during a particular season, the more likely (and shocking) their death will be at the end of the season. (e.g. Ned Stark as the great father and immensely honorous man S01, Rob Stark as the young, charismatic general who married out of love S03, Oberyn because duh S04 and now Shireen, who has had a much more prominent role this season than all the previous ones combined, as the beloved, cute, literate, etc. daughter (by everyone except her mother that is))
Shout by Brian MaloneyBlockedParent2015-06-08T02:14:02Z
It's clear that the writers value shocks and twists over characters with consistent motivations.
Edit: I'll remember Stannis as he was.