St Augustine was wrong on many points, and the West was to dependant on him. However, one man's voice is not the voice of the Church, especially when you consider the East's opinion of much of Augustine's writings.
Danfrey said:
Chrysostom
"never be afraid of the sword if thy conscience does not accuse thee: never be afraid in war if thy conscience is clear"
Are you sure you are reading this correctly? Let's leave the quotation in context:
So then I fear not an enemy’s plots: one thing only do I fear, which is sin. If no one convicts me of sin, then let the whole world make war upon me. For this kind of war only renders me more prosperous. Thus also do I wish to teach you a lesson. Fear not the devices of a potentate, but fear the power of sin. No man will do thee harm, if thou dost not deal a blow to thyself. If thou hast not sin, ten thousand swords may threaten thee, but God will snatch thee away out of their reach: but if thou hast sin, even shouldest thou be in paradise thou wilt be cast out. Adam was in paradise yet he fell; Job was on a dung hill, yet he was crowned victorious. What profit was paradise to the one? or what injury was the dung hill to the other? No man laid snares for the one, yet was he overthrown: the devil laid snares for the other, and yet he was crowned. Did not the devil take 255his property? Yes, but he did not rob him of his godliness. Did he not lay violent hands upon his sons? yes: but he did not shake his faith. Did he not tear his body to pieces? yes but he did not find his treasure. Did he not arm his wife against him? yes but he did not overthrow the soldier. Did he not hurl arrows and darts at him? yes but he received no wounds. He advanced his engines but could not shake the tower; he conducted his billows against him, but did not sink the ship. Observe this law I beseech you, yea I clasp your knees, if not with the bodily hand, yet in spirit, and pour forth tears of supplication. Observe this law I pray you, and no one can do you harm. Never call the rich man happy; never call any man miserable save him who is living in sin: and call him happy who lives in righteousness. For it is not the nature of their circumstances, but the disposition of the men which makes both the one and the other. Never be afraid of the sword if thy conscience does not accuse thee: never be afraid in war if thy conscience is clear
Is St John advocating that Christians take up the sword? Or, is he telling them not to fear when someone takes up the sword against them?
In the very next paragraph, he states:
I was the subject of his plots, yet I became his protector. I suffered countless troubles at his hands, yet I did not retaliate. For I copy the example of my Master, who said on the cross, “Forgive them, for they know not what they do.”
Is he advocating 'Just War'?
Elsewhere, he writes:
“So long as we continue to behave as sheep, we are victorious. Even if ten thousand wolves surround us, we conquer and are victorious. But the moment we become wolves, we are conquered, for we lost the help of the shepherd. He is the shepherd of sheep, not of wolves. These are his words: ‘Do not be troubled that I send you out in the midst of wolves and tell you to be like sheep and like doves. I could have done just the opposite, and not have allowed you to suffer any hurt. But I chose a better way. My way makes you more glorious and proclaims my power.’ These were his words to Paul: ‘My grace is sufficient for you, for my power is made perfect in weakness. That is the way I made you.’”
and
Christians above all men are not permitted forcibly to correct the failings of those who sin. Secular judges indeed, when they have captured malefactors under the law, show their authority to be great, and prevent them even against their will from following their own devices: but in our case the wrong-doer must be made better, not by force, but by persuasion.
I think you may have misrepresented St John Chrysostom.