These lyrics are fairly cryptic to a degree. I don't believe they can be fully understood simply because I believe the entirety of the song is a musical interpration of the short film(music video). If we interpret the first verse as describing how the witch must be hung under accordance of the church, then we can come to an understanding that the young man had a personal relationship with this witch because of the way he acted. However, this is a metephor to the difference between the people of the world. In this case the dominating power(church/organised religion) have seen the witch as an independent and ever developing individual. Of course individuality is important, as it is what drives creativity and in turn, progression within a society. Essentialy I take this song as a metaphor to all the power hungry bodies desiring the ability to stop individuality, as controlling the conformed masses is a lot easier. Now, the boys part in the song can be the interpretation of those who can see past the brain washing and can trully apreciate individuality. That is why he loved the witch. When he was takin from her the second time, the priest yet again tried to reintergrate him into their idea of society. When he went to beg for her life he was denied(as expected). He then realises that he must gain the priests trust before he can gain his revenge. So he agrees to execute his love for good. Once it is done he reveals his plan and burns the priest alive. Thus, forfilling tge metaphor that in this modern age we have begun an enlightenment into world religious and corrupt politics. However, to reject this idea of a conformed world we are bound to be reconvinced or re-brainwashed and perhaps the best way to bring down the corruption is to manipulate it from the inside.
Perhaps I am thinking too much. But this song makes me do that.