I think what i really like about the merlin official twitter making both King and Lionheart and A Thousand Years merthur songs is that the two songs depict different types of relationship.

King and Lionheart is from the point of view of a sister who's brother has gone to fight in a war. A Thousand Years was made to accompany a marriage scene. One relationship is platonic, the other is romantic.

Perhaps unintentionally, it becomes an indirect acknowledgement to the way people wish to interpret Merlin and Arthur's relationship; that both interpretations are appropriate and one does not nullify the other.