I quess so, since you said the same commander defeated two of your ninjas.
EDIT:
Addition to the above: it's probable that if assassinations can happen more than once, they aren't limited. It'd be extra work, at that point.
I'm not sure how assassins work, especially multiple ones. What if the assassin that did nothing targeted the commander that was successfully assassinated? With his target already dead, he wouldn't have anything left to do. I really doubt it works like that, but that might explain it.