No she didn't. Brahne only knew what Kuja told her, and all he bothered telling her were things that would appeal to her nature: AKA dem things blow up. Coupled with the fact that Brahne was a bitch, it's safe to assume that she told Beatrix bugger all about anything. She wouldn't and didn't know that the process was forcibly removing something that was a part of Garnet, either.

You're thinking like you, which is why your argument is so fail. I'm not gonna bother arguing that killing innocent people minding their own business is a great way to test a weapon, because it's obviously wrong. But if you were Brahne, some power hungry psycho looking to forcibly take over the Mist Continent, then yeah I think it's an okay test method.

We also already know that Beatrix is a blindly loyal soldier. That's...well, that's exactly her character and the point of her inclusion in the game. The whole concept is that she's just a big, powerful robot. But she starts having doubts because Brahne's a massive dick, finally culminating in her betrayal when she rescues Garnet.