That line about Bonney needing protection really makes it seem like she's going to stick around, so perhaps we're getting a new crew member? I'm still not over Carrot and Yamato but I wouldn't complain if it happened.
I've been of the opinion that Bonny will join ever since we learned that she's an orphan who was raised by a father figure that would later sacrifice himself for her without her knowing. Prime straw hat backstory.