Are you kidding? Server owners pay for their server and have the right to say what is okay and what isn't, what is enabled in the configs and what is not. Generally, they are the only ones actually putting real money into the server, and they have to deal with all the technical issues, and moderating issues between the players. It's a lot of work. Some do it better then others, but it's still a lot more trouble than any player who is simply playing on the server has to deal with. Sure, a player may not like how an Admin runs a server, but at the end of the day, it's the admin's server. If the player doesn't like it, then they can do as you said, and leave. A player should only have a say in how the server is run if they've actually put money into it.
You say that letting admins remove the bedrock sword's armor damaging ability is abuse? Not all armors use their durability. Modular Powersuits uses a charge to determine whether it's armor is working. Your sword bypasses that feature and destroys armor that is supposed to be indestructible. THAT'S an exploit. This exploit also affects IC2's nano and quantum armors, and Blood Magic's bound armor. It likely affects many other things that aren't in FTB as well. The only things it doesn't affect are KAMI's ichorcloth armors and IC2's solar helmet. Your bedrock armor was technically affected, but it's massive durability makes it not matter. Even for armor that does use durability, your sword basically wrecks it. Your sword basically makes almost every armor added by other mods worthless in pvp, at least from a defense perspective. It's almost as if the whole point of it is to make all other armors worthless so people have to use your bedrock sword and bedrock armor in order to stand a chance in pvp.
As far as your logic for not having config options for the Bedrock sword and other features go, it's flawed. Not having a config for certain features won't "force" the server admins to let the players use them. If an admin doesn't like an item or feature and there isn't a config option for it, they can just make a rule saying that players can't use it. If a player is caught breaking this rule, they would probably have to destroy the item, or be banned. Having a config option seems like a much better alternative than that, imo.