All Brotherhood shoot ghouls on sight. Sure they may not go out of their way to hunt and kill them but if they come across them they will. They hate Super Mutants. Lyons killed off the people of pittsburgh for being to mutated.
The work camps of the MWBoS are mostly filled with raiders and slavers so its their way of dealing with criminals. They did start letting mutations join which goes against the brotherhood policy toward mutations. Now its not hard to see that not all those within the MWBoS were happy with this, seeing it as a step to far. MWBoS are doing the next logical step that Lyons might someday do. They take control of settlements and they do help. They share tech but they arn't going to just hand it over for free.
Now Barnaky does not like Mutations so he stops letting mutations into the brotherhood. He treats them like humans in the wasteland treat them. There was a mission cut form the game called "Springfield" and in that the mayor talks about how "ghouls are second class and so on." Barnaky's actions would cause the down fall of the MWBoS which explains "Fallen on hard times" we learned about in Fallout 3. It would also give us "The Mutant Liberation Army."
MWBoS have also been around 80 years before Lyons, he was not even born when they formed. No other ending to Tactics would explain how they went from a large group bigger then just a chapter. A group that allowed outsiders and even mutations and then taking control of the Calculator, to small group outside of Chicago. Which I hope they are still a very big group but just in hidding.
Even if they go with the ending were they did not gain control of the Calculator there would be no reason why they "have fallen on hard times." They let in outsiders and mutations and have been around for 80 years. They have bases across the Midwestern United States. From Chicago to Colorado Springs. The only ending to Tactics which would explain their "down fall" is the Barnaky Ending.
This is the Midwestern Brotherhood of Steel's policy ===> http://www.youtube.com/watch?v=GtXhuaTcohY.
( I know how your hard to convince of things Styles, so i have been looking up info for you for proof to back my point that the calculator ending makes the most sense, i cut and paste this out of the General Barnaky entry from the Vault Wiki:
Barnaky's Fate
There are three possible ways the General's story could end.
* Depending on how the player chooses to deal with him, he could come back to his senses after the Warrior reminds him of his wife using his locket or his holotape. Now Barnaky becomes scared of his betrayal, his new form and human extermination. After this, the Warrior could put his brain into the Calculator, which then takes on a pro-Prime Human mentality and begins to restore mankind to its prior glory at the cost of all mutated beings and Super Mutants being hunted down and chased back to the West Coast.
* He could be destroyed while fighting the Warrior.
* His fate if the Warrior saved him then decided to sacrifice himself to become one with the Calculator is not known, though it could be assumed he becomes the guardian of the Warrior/Calculator, or is executed by the Brotherhood.
According to Rothchild in Fallout 3, the canonical ending of the game is the slow downfall of the Brotherhood which could be a result of the destruction of Calculator, so it could be assumed that Simon Barnaky's canonical fate is death by the hand of Warrior. I also got this from the Calculator entry from the same sight:
Menace from the WestEdit Menace from the West sectionEdit
The Exodus protocol could also be triggered by a breach of the vault's defenses, as was the case when the Eastward-fleeing super mutants stumbled upon Vault 0; this awoke the Calculator completely. The cybernetic being proceeded to enact its "pacification protocol", considering all life to be its enemies. The Calculator activated its nuclear reactor in Buena Vista and constructed many robot manufacturing and repair facilities across the wastes. Soon, the Chicago region was full of rumors of a Menace from the West, coming to exterminate all life.
The Calculator discovered a useful ally in a captured Midwestern Brotherhood of Steel General named Simon Barnaky, who began to see the machine as the only hope of restoring order. Barnaky was transformed into a humanoid Robobrain and began his service to the Calculator as its adviser and guardian.
Although the Calculator had begun rapid expansion and had attempted to eliminate the Midwestern Brotherhood of Steel, Vault 0 was breached by Brotherhood forces led by the warrior. There, the warrior defeated the robots and Simon Barnaky's new form, and entered the Calculator chamber. The eight brains crucial to the Calculator were destroyed, so the Calculator required a new brain to continue to function. From here on, the warrior had three choices.
* Merge with the Calculator, taking control of it and using its resources for the Brotherhood.
* Allow Simon Barnaky to merge with the Calculator, which would result in a new Brotherhood of Steel and anti-mutant regime.
* Do nothing, allowing the Calculator to shut down forever, or destroy it using weapons.
In Fallout 3, it was revealed that Midwestern Brotherhood of Steel had fallen on hard times, so it is believed that the canonical choice the warrior made was the third one. Also, i looked up the Warrior as well, just for the fact i like to do things in threes:
The following is based on Fallout Tactics and some details might contradict canon.
The Warrior was the nickname of the Player Character in Fallout Tactics.
Background
Unlike the Chosen One, the Warrior was not a descendant of the Vault Dweller or any of the Vault 13 people. He/she was a tribal recruited by the Midwestern Brotherhood of Steel as an Initiate. General Simon Barnaky believed the recruit would be a great commander, and after all, he was right. The Warrior successfully accomplishes one mission after another, faster than anyone before, achieving new ranks. Later, the Warrior became a legend in the Brotherhood and a new General.
It was the Warrior who won the faction war that took place in Chicago, by defeating the threats of an alliance of local raiders, a psychic tribe of Beastlords, who were able to control animals of the wastes, and Gammorin's super mutants, the remnants of the Master's army. However, the Warrior's greatest deed is winning the war against Calculator's robots. In the end, the Warrior either became one with the Calculator, allowed someone else to do this, or simply destroyed the Calculator.
Judging from the Fallout 3's information about the Midwestern Brotherhood of Steel, the Warrior probably chose to destroy the machine. Since I will more than likely be ignored anyway, I will only add you are right, i checked the timeline and you were right about Lyons not being born yet. But Vault Wiki Has all the info of the Bible already, and every other source that has been put out there, i have been scouring as well to confirm their info. It's the most logical choice. I know you want the Barnaky ending, but it does not make sense, you can't get out of things that easy by depending on an all knowing computer, humanity has to learn the hard way, and the calculators destruction does fit the mutant status quo relatively fine as well, while sticking to canon as well.)