I never got that impression, that a thesis of the comic is "War is bad." Certainly, it portrays "War is hell." But so it is in our real world. And just as in our real world, war can be viewed as morally ambiguous. For example, most people would view defensive war as justified though of course then the argument of what constitutes a defensive war can be brought up. In the comic, the ambiguity of war is evident in opposing viewpoints, eg Tool as Worm vs Tool as The Chosen of the Titans, rule by nobility as inherently good vs nobility as inherently bad, war as part of Erfworlder's innate makeup vs war as a conscious choice in Erf, war as rightful duty vs war as a compulsion. These competing theses interact with each readers own viewpoint further complicating the issues.
It seems to be that Erfworld treats many other themes in the same way, not just war, but also love, gaming, reality and illusion, etc. If anything, the overall theme of Erf is itself, or rather self-reference to itself, how we the readers relate to Erf relating to the real world reflects and is reflected by how we relate to the real world. As such, Erf is meta-fiction. Interesting. I'm reading the late David Foster Wallace's essays in "A Supposedly Fun Thing I'll Never Do Again" (1997) in which he comments on meta-fiction in TV and literature.