@Starstruck
I agree, she's not one to spare innocent people for no reason. She DOES seem to have a soft spot for kids in general, but Mary obviously doesn't count. I think she wants the organization to fall, but she's definitely not going out of her way to do so. The possibility of Mary surviving and becoming an ally to Conan seems like a low-risk gamble to me, since either it works and he gets an ally, or Mary just dies. No major loss to her personally.
That said, I ended up writing a more detailed post on a DC forum after posting here, and while writing it a thought occurred to me that she may have been specifically ordered to use the APTX-4869 after all, and carried out the confrontation the way she did in order to make sure there would be no body. Basically, the amnesia story bugs me because it's the flimsiest excuse possible. I think she intentionally chose a weak story to make Mary suspicious from the start and force a confrontation there by the river instead of waiting to go to a more secluded place. That way she could throw Mary's body into the water after giving her the drug, so she'd be just as likely to drown before the drug killed her and thus avoid suspicion if her body washed up somewhere. If no body is ever reported, that's even better.
The key motivation would be to make sure the Black Organization wouldn't need to recover or care about the body. If she DID survive and turn into a child, the BO would obviously take a look at all the other victims, and there's already been a lot of suspicion about Shinichi in the past. It wouldn't take long to find Conan and make the obvious connection, and since he's living with Ran they'd BOTH be in immediate danger.
Perhaps a bit of a stretch, but I do feel like Vermouth had SOME extra purpose here. Seriously, the amnesia story is so full of obvious holes, it's like she was barely trying with it. As someone who specialized in disguises, her acting felt completely off.