Natural Law does not assume or demand pacificism. It doesn't demand adherance to theology. It doesn't take sides in any particular conflict. Natural Law is self-evident, observable law.
It ascribes a very high cost to the use of violence (because violence does carry a high cost, this is self-evident), so that beings are disinclined to use it. Also, it can be used to uncover what is the most orderly outcome, that will assert itself naturally over time, so that individuals can simply pursue that outcome and be ahead of the curve.
It also assumes that different actors can view the same situation differently, so that both sides see themselves as the most-aggrieved party. One man's freedom fighter is another man's terrorist, for example. Both sides can plausibly and convincingly claim self-defense.
Natural Law demands that we accept this moral ambiguity because we have no chance, but to accept it. Because it simply is. Because humans are complex, life is messy, and we are not omnipotent.