Aren't runes when activated, instantaneous spells? If so in the description of Counterspell it says this: "When used it attempts to disrupt the matrix of magical energy being formed by another spell user." How hard is it to counterspell an instantaneous spell?
I would think then if someone would try using counterspell to disrupt the instantaneous casting of a rune it would be at a great difficulty, very hard (-60) or higher, and only if they knew it was going to happen.
Timing would be essential. "Who wants to try and grab the cheese from that mouse trap?"
IMHO.
Bruce