I don't think that's how it works, Leif. Every time I've played or DMed a rune priest, they have access to both runes and they pick as they use a power which one they're using.
The compendium's description says, "Some of your powers have the runic keyword. When you are going to use a runic power, you first choose one of the runes noted in the power—either the rune of destruction or the rune of protection—and then use the power, applying the chosen rune’s effects. The moment you choose the rune, you enter its rune state."
I read that as you can use Destruction this round and Protection next round with the same at-will power.
You might be confusing it with Runic Artistry, wherein they select one of the paths of runic power (wrathful, defiant or serene). That one they only get one of, and GH has chosen the Wrathful Hammer option.