"It is at all times a part of the task of the people of God to destroy evil. Once we see this we do not, for instance, meanly apologize for the imprecatory psalms but glory in them." Cornelius Van Til
Obviously we must temper this sentiment with the whole counsel of God. I am by no means an expert in this area of theology, but I would suggest that when dealing with the leaders of nations that we should always pray for repentance first; but if it would appear apparent that God is not granting repentance I think we are not only at liberty to pray such prayers but rather that we are responsible to do so. I am saying this, of course, in the context of a just cause for war.
The only book I know on the subject is War Psalms Of The Prince Of Peace by James Adams, who is not to be confused with Jay Adams. My copy was published by P&R. They are only related in Christ, but Jay Adams did write the forward to the book, strangely enough.