From my understanding of Ai/Shiho's personality, if she were confronted by any BO member, she would rather "submit" herself to the BO instead of fighting back against them. On multiple occasions, her allies (especially Conan and Ran) had to save her from death at the BO's hands. Furthermore, her ingestion of the antidote and reversion to her adult form is part of her plan to surrender herself to the BO. Why, then, would she attempt to "fight back" against Bourbon?
I didn't necessarily say she would fight back against them, but if Amuro made the first move and pointed a gun at her, Shiho would probably buy some time by entering Room 8B. That would be the perfect time to grab the gun with the silencer and either point the gun at herself or at Amuro in order to catch him off guard, not to fight back against him and actually shoot the trigger.
We also have to take into account that she DIDN'T want to participate in the Witness Protection Program when Jodie offered, which shows signs that she IS willing to fight against the BO. Even though Haibara seems to have regressed back into her paranoid state in this arc, I could only imagine that she will disregard her fear of the BO and fight back (in one form or another). If she does "submit" herself to the BO like you suggested, then there would be no character development; the inner strength she has developed throughout the course of the series would all go to waste.
As for the antidote, Haibara decided to use it JUST IN CASE she is killed by the BO, but it doesn't mean there's no more fight left in her.