"If the tradition which claims that war may be justified does not also admit that it could be unjustified, the affirmation is not morally serious. A Christian who prepares the case for a justified war without being equally prepared for the negative case has not soberly weighted the prima facie presumption that any violence is wrong until the case for an exception has been made."
– John Howard Yoder, When War Is Unjust: Being Honest in Just-War Thinking
Curious Christian 
Yoder’s logic makes a lot of sense to me here.
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Flowing from this, just war advocates, if they are morally serious, should be just as committed to selective consciencious objection as pacifists are to blanket consciencious objection.
There are some problems with modern day application though, as Catholic theologian and just war advocate Drew Christiansen admits:
“Finally, we must concede that the social and psychological conditions for making just war reasoning effective as a system of social constraints are lacking [in comtemporary America]. The absense of protection for selective conscientious objection is a major deficiency, but to that must be added (amongst others) the lack of accountability of air power, the absense of the habit of resignation in protest, and the need in public institutions for conflict resolution and training in nonviolence.”
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