Having done this initial Myrmidex vs. Eodonians fight a few times now, I have to say I do NOT like how it works.
I asked my friend to join me to work on the new quest. She and I were fighting on the Myrmidex side and had made pretty good progress when a couple guys came in on the Eodonian side. There was no point continuing--we were at a stalemate. So we left.
My friend has said that she won't be doing that quest again at all, and I can't blame her--if everyone doesn't pick the same side (which, let's face it, will usually be Eodonian since the banner is right there at the entrance) then it's going to be a major pain, especially if both sides are roughly evenly matched or if you happen to be in the smaller group. That's a frustrating mechanic to deal with at all, let alone a repeatable quest. Grinding 3+ hours of fighting for a single quest just isn't fun.
I got a bigger group and am waiting for the respawn... but the fact is that I had to literally stop and wait for the other side to finish. I couldn't proceed with my quest, and I couldn't switch sides. I could have kept fighting, but where's the fun in an endless stalemate? This is just frustrating.