Your not taking into account the perspective of Beatrix. We know that the Eidolons are part of her life force. We know that the horn isn't a vital organ (we saw Garnet alive afterall). But when Dr. Tot recalls the removal he says, "The girl cried out in pain...". The Alexandrians had no idea what they were doing at the time.

Quote Originally Posted by PuPu View Post
]And she totally ignored all those doubts she had about Brahne and continued to spout blind loyal soldier nonsense such as "I'll kill all enemies of Alexandria!" until the very last minute where the plot forced her to become an ally.
There's a difference between a plot being "forcing" something or the storyline "forcing" something. Beatrix wasn't just going to betray Alexandria because she had doubts, all soldiers have doubts. Beatrix made her choice when the need to make one was thrust upon her. Even when Brahne said, "the girl is useless to me" Beatrix was going to deny that meant she was going kill her. Its like when a president signs to go to war, it'd be much different if he was pointing an M1 Garand at an 18 year old kid's head.

Quote Originally Posted by PuPu
Quote Originally Posted by Goldenboko
They removed her horn when she was a baby because the assumed it was the best for her, to someone who doesn't know about Summoners, that would seem a lot more painful then removing intangible creatures.
...no it wouldn't. Considering that a horn isn't a vital organ or anything like that, and that her Eidolons were essentially part of her life force. Also, "intangible creatures"? Odin destroying Cleyra wasn't intangible.
Yes, I know what a plane is, I don't know how it flies.
Odin.
I said HOW IT FLIES. I know it smurfing flies, but I don't know which wire will plummet the plane to the ground if I clip it.

As for unjustification, soldiers do horrible things. I'm not going to debate that, it doesn't make her a bad character in game.

Quote Originally Posted by PuPu View Post
She wouldn't and didn't know that the process was forcibly removing something that was a part of Garnet, either.
...lol. She couldn't figure that out from "Extract the Eidolons from Garnet?"
I can have a gun stuck in me and Dr.'s nowadays could remove it without killing me. Same concept she doesn't know it will kill her. You're taking facts you know as the audience and assuming the characters know them.