Having given some thought to the odd conundrum we find ourselves in where some alliances put up free rails, which is obviously to the benefit of the players, only to have those rails immediately challenged (the counterargument being: why not?) I realized that the answer is pretty simple.
There is one basic principle at play here. Players want credits and resources. They will settle for battle pay if there are taxes on the rail. Contenders for a rail who want to tax it will often put up battle pay, and those who want to keep it free will not be able to do so forever if they can to begin with. The solution is simple: treachery.
In the real world, treachery is punished harshly. Practically everyone worldwide hates a traitor and the usual punishment is death, even in countries that otherwise have abolished capital punishment.
In Warframe, this system is broken in that there is zero punishment for betraying anyone. If someone wins a rail and sets an exorbitant tax, do not run missions for that alliance's rail and when it is inevitably challenged, do accept their battle pay. Run perhaps five missions for your allies and three for your enemies so their rail still dies and you help to deplete their battle pay. This will keep the rail taxes low for when they're not at war and discourage higher taxes from ever being set in the first place because nobody will be able to keep up high battle pay forever if they keep losing rails trying to do so.
When fighting for or against alliances in the Dark Sector bid, simply ask yourself: What would Darvo do?