The intent isn't for runes to be hot-swappable or interchangeable at any time. The ability to change the rune is the point of any comments made about switching them around, not that we want to allow easy and free interchangeable runes. What we do intend is for people to be able to try different runes without fear of losing the rune, or permanently changing the way a skill works.
Early design thoughts on rune swapping are that there would be some sort of cost to remove them so a new one could be put in its place. Early in the character's life it would be inexpensive enough so it isn't prohibitive, as we want to encourage experimentation, but later on the cost would become more substantial.
In addition, the high end runes are intended to be very rare. So while you're looking for them we want you to be able to use the runes you have without fear of losing them or using them incorrectly. Being able to experiment with different runes along the way to creating your perfect character is more fun, and potentially enlightening to the different ways your character can be used.
He also went on to say that it hasn't yet been decided on if the "some sort of cost to remove them" will be entirely currency based or something else. I definitely like that they have it set up so you'll be able to experiment with the runes without worrying about using them improperly. What do you guys think?