I read part of the article you cited - up to the point where it became obvious the author hadn't read, or hadn't comprehended, Michael Walzer's Just and Unjust Wars. (I should point out that I've read it three times over the last 20 or so years. I didn't recognize it from what the author attributed to it.)

By that point, it had also become obvious he was more interested in attacking a caricature of Just War Theory than in critiquing its reality. I suggest you read Walzer, and then dig into some of the more balanced discussions of JWT. The Wikipedia entry provides a good starting point.

(On a side note, when reading anything by an Objectivist, its a good idea to do your own reading of whatever they're attacking. They frequently attack straw men.)