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The drugs should work well enough to where Jack wouldn't remember much of the actual operation, but the facts of the matter were that they couldn't actually make him fall asleep for his amputation due to his condition.
O'Brien knew she didn't need to be there with him, and they would eventually kick her out to properly perform the amputation on his leg, but she stayed with them in those early moments.
One of the EMTs handed her a thick cloth and told her to put it in his mouth for him to bite down on to muffle his screams and provide an outlet for him when the pain would inevitably hit regardless of how much local anesthetic they put on his leg.
She went over to him and gently placed the cloth in his open mouth. "Bite down on this" she instructed, hoping it would break through the feverish state he was in. It took him a moment, but he eventually complied, securing the cloth between his teeth. She smiled. "Thank you" she said quietly. And then, "It's gonna be okay, Jack"