Everyone is selfish when it comes to having their "fun". Good db players will ask to enable db and the ones who hate chainsaws might suggest to remove them. Great pilots might even suggest extra rustlers at civ spawns for them and that too will be affecting the gameplay of others but hey! Who cares? Selfish 
And here we find the problem. People who don't shoot each other when they should don't care about fairness, they just care about themselves.
There's a major difference between your examples and enforcing the rule against helping the opposite team. DB, chainsaws (to an extent) and Rustlers are all things that everyone can use, regardless of their social status in the server. They're all something that is understandable and fair in that I can be a good DBer, have DBing shit added, but people can use that against me as well.
In contrast, you have to be part of a special group which has conspired together to make an alliance. You can't magically conjure up an alliance with the opposite team and use it against someone else. Someone without an alliance can't kill you while your friends watch and do nothing, but you can do that to them, if their teammates are also your friends. You also have to have knowledge of the alliances to even know how to avoid the shit that gets pulled. I had no idea IDF and GgT had a non-aggression agreement until I got killed by a GgT cop without an IDF terrorist teammate doing anything to stop it. I had to ask if they were "allied", and unsurprisingly they were. Explain to me how this could possibly be fair, or reasonable? The only thing you can say is that I could make my own clan, but that isn't solving the problem, is it? It's just pushing the bullshit to people who have even less power to retaliate.
While you're at it, someone explain to me how this will "destroy the server and/or the gamemode". I'd love to know. Would something as simple as just having "allied" players on the same side really ruin anything? Again, elaborate.
Difficulty of enforcement is not an excuse (if there is even that much difficulty), and just the fact that people are resorting to that argument should tell you something. Just because there are "gray areas" doesn't mean that the black-and-white shouldn't be addressed.
The "it's been this way for X years" argument is absurd. I guess what I should take from this is that clans have been breaking the rules for X years, and that long-established clans don't really deserve my respect because they've built their reputations on this shit?
You can claim again that I'm taking things too seriously and overcomplicating the issue, but I see walls of unsupported bullshit spouting from the pro-alliance side, none of which addresses what should be the core issue: is this behavior fair?
Poll