Herfrom - no, a different theory.
Duckdaemon (love your name btw) - was that the Forbes one where the reviewer was virtually spitting blood? Y'see, I think it IS in character for Stannis (see my earlier post) and I think the scene was done precisely to keep us off guard and I think he did love her in his way, because for a sacrifice to be a true sacrifice it has to be a real sacrifice of something he loves. The act of sacrifice has taken on a meaning distinct from the word's actual meaning - now we view it as simply meaning 'execution' or being mildly inconvenienced, but it really refers to an act of giving up something important. Hence in classical times (the Illiad) and biblical times a child would often be sacrificed, because it needed to be a true sacrifice of something loved or the gods wouldn't be impressed by the fielty.
Also, in that earlier scene Stannis tells her 'you are my daughter, the princess Shireen of Baratheon' - everyone took that to mean that he loved her and was proud of her. Did he actually say that though? Even during that episode I thought 'we're being reminded she's important to him because she has royal blood, nothing more,' and we all know what royal blood can do.
Personally I have no problem with the validity of this scene or any other, although I found it very distressing. There is historical, classical and modern precedent for all we are seeing - it may be a fantasy but it holds a mirror up to our world, past and present. The whole POINT of the books/ show is that life is hard, random, meaningless, we fight the wrong battles, we make bad choices, we are human. Good people die, bad people succeed, but also no one is truly good or bad. Terrible things happen in the name of power, money and religion and there is no inherent kindness in the world. I think it's very deep.