Anyone correct me if I'm wrong but doesn't it work off the mechanics of regular arrows, thus having high hp to take the hit and survive or high armor to absorb the hit will save a commander.
Not sure if things like equipped shields or the Clock of Missile Deflection help. Lets try searching....
Yay!
Ok so some great testing done by the knowledgeable Calahan, the key point for this discussion being:
"The end results show that out of 300 'Seeking Arrows' cast at....
300 Bare Scouts --- 151 died, 45 received afflictions.
300 Scouts equipped with a Small Shield (Parry 4) --- 150 died, 39 received afflictions.
300 Scouts equipped with a Tower Shield (Parry 8) --- 145 died, 57 received afflictions.
300 Scouts equipped with a Lucky Pendant --- 67 died, 25 received afflictions.
300 Scouts equipped with Robe of Missile Protection --- 14 died, 9 received afflictions."
So it seems shields do nothing, Lucky Pendants seem to stop 50% (as you would expect if they did anything) and Robes of Missile Protection are awesome. CBM changes Rings of Warning to have I think 50% missile protection so they may be an option. If you have an air bless then Shrouds of the Saint may be an option too.
Realistically....
Put these items on those you really want to protect (mages with cool names and the like

) and spam indy commanders to protect the rest.