That might seem fairly inconsequential, but it's really not. You see, one of the natural barriers to a militia totally dominating their warzone is that once you've captured all the systems, you no longer have any systems left to plex in and your ability to make LP is curbed unless you decide to run missions instead.
However by plexing against your opponent's allied faction instead of your opponent directly, you can still have access to contested systems regardless of the situation in your own warzone. For example if the Minmatar militia were to completely dominate the Min/Amarr warzone, they could still plex for LP by plexing in Caldari systems. The ideal situation would be if two opposing factions, for example the Minmatar and Caldari, both dominated their respective warzones - both sides would have the maximum number of potential systems to plex in, while each maintaining enough systems in their own warzone to have almost constant T4 or T5 warzone control.
Now, imagine that in this purely hypothetical situation where the Minmatar control almost all of their warzone, you were fighting for the Amarr militia. You could keep on fighting the good fight against the Minmatar, sure. Or you could switch to the Caldari militia. You'd still be able to shoot exactly the same people as before, plex in the same systems as before, and dock in the same stations as before. The only difference would be that instead of cashing in Amarr LP at terrible prices, you could cash in Caldari LP at fantastic prices. Unless you're a hardcore devotee of your current faction, it simply makes sense to switch - you probably have the standing for it already on account of them being allied.
In the current game mechanics I believe that this, not any of the examples listed in my original article, is the natural equilibrium point for the new Faction Warfare system. It's also fairly close to coming true - the Minmatar and Caldari are both currently on the ascendant in their respective warzones, and recent news suggests that Fweddit, currently the mainstay of the Amarr militia, are in the process of moving to join the Caldari.
Is this a bad thing? That depends on your point of view. Achieving this kind of equilibrium would mean that pretty much anyone who wanted to could roll a low skilled FW alt and make bucket-loads of isk by orbiting buttons and cashing in their LP at excellent warzone control tiers. Eventually this would drive down prices for the LP store items (including items also available in non-FW LP stores), however I expect the level of take up would never be enough to make it anything less than 'ridiculous money'. What I would definitely say is that it isn't an intended outcome. I'll be very interested to see how this plays out!