The message of Peacekeeper Wars might be a bit frelled up, honestly...
*OBVIOUS SPOILERS*
Yeah, I know there's a board for PK Wars, but this one is much more active.
I watched the miniseries with my Dad, who enjoyed it as much as I did, but at the very end he said something like "so, the moral of the story is that you have to use a weapon of mass destruction to show how bad it is." And I started thinking a bit about that.
In Farscape's third and fourth seasons, when the plot of the search for wormhole weapons became center stage, it felt like the writers were trying to show how futile and destructive the idea of an arms race is. By the end of season 4, there are some major references to Dr. Strangelove, a movie that treats nuclear war like a ridiculous farce, such as John writing "hi there" on the Katrazi atom bomb. This seems to suggest that the writers wanted us to think of the quest for WMDs as violent lunacy, and that the right thing to do is to look for alternative options and ways to stop it (even if it involves destruction itself, like the Command Carrier disaster in Into the Lion's Den.).
And Peacekeeper Wars seems to at first support this sort of doggedly anti-war philosophy, with the Moya gang rounding up the Eidelons for their peace-inducing powers...but then things go haywire and John has to deploy the wormhole weapon in the battle as a last resort, much to others' protests. Yes, you could argue the crew is backed in a corner and has to either take a crazy risk or die (sort of like crossing the streams in Ghostbusters or activating the Omega 13 in Galaxy Quest), but this is a bit different, as this is a terrible weapon and we see it doing its job by destroying many ships and the planet below (hope they evacuated all those surviving Eidelons!). Then John says that weapons don't make peace, but people make peace...but in this case, the threat of the weapon played a pretty big part in it! The triumph of peace becomes a bit less poignant when the two sides are forced into it by a crazy man with a weapon.
You could compare it with the atomic bombings used to force Japan's surrender in WWII, but in that case, the introduction of a heinous new weapon led to countries around the world buying nuclear arsenals, while in the miniseries...the Ancients swoop in and wipe all of John's wormhole knowledge so no one can ever make one of those big nasty weapons again. How convenient!
Now, I really love Peacekeeper Wars, and I don't think this message is really a political screed from any of the writers so much as it's just implicit in the narrative. But still...I'm sure other people have had the same thoughts on it I've had, yes?
What I think of your post: https://m.youtube.com/watch?v=VC4YjOp4Cto#t=10s