Answer

First of all, the fact that something is permitted does not mean it is morally positive. It only means that there is no halakhic prohibition. A father is also permitted to give his daughter in marriage to a man afflicted with boils.
Beyond that, states and nations go to war for all kinds of reasons and interests (in the sense of “stretch out your hands against the troop”). The Torah grants permission for this, because a functioning people must have that option. The judgment has to be made with good sense and reason, since these are matters of life and death. For example, suppose a neighboring people stole a few kilometers of our land. Does that justify a war? Seemingly there is no commandment here, nor a danger to life. But there is a legitimate interest here, and preserving our standing as a people and as a state. Therefore this is a legitimate war.