It is currently not possible to override the default runebar element's Update, you have to make a custom element if you are not happy with it. But Haste wants to merge Runes, Druidmana(now used by Mistweaver monks too) and other class resources represented by bars, so things will soon(tm) change.
With the default element you could use self.Runes[i].bg and color it differently so that you have more contrast when the rune is on cooldown. Phanx argument, that it is probably not easy to distinguish 90% from full on very small elements, remains (PostUpdate would help here, that's true).
Apart from that you could use
lua Code:
colors = setmetatable({
runes = setmetatable({
{0.69, 0.31, 0.31}, -- blood
{0.33, 0.59, 0.33}, -- unholy
{0.31, 0.45, 0.63}, -- frost
{0.84, 0.75, 0.75}, -- death
}, {__index = oUF.colors.runes}),
}, {__index = oUF.colors})
to change the runes' colors if you have problems distinguishing them.