@I:
Well I've said this before, but it bears repeating. BB was still in ID after Luffy and his gang left. We know they created a major less and left Magellan so injured he ended up in the hopsital. The timeline for all that is what we do not know. When last we saw Bon0chan, he was in the control room and Magellan was getting ready to… take some sort of action--what sort of action, we weren't not privy to, although most would assume poison. Now, if BB made a critical move/arrived at or near the control room at the right moment, Magellan, as the chief warden, would presumedly have been forced to delay his intentions to handle that much more dire situation immediately. I will remind you that Bon-chan was not wearing kairoseki cuffs, nor was he bound or held in any way at the moment when we left him last. If there was chaos, or even if the people in the control room took their attention off of Bon-chan for a split second, he could easily have turned himself into any one of dozens of ordinary jailkeeps that work there–I'm sure he fought (and therefore touched) several, so he had their info--slipped out of the room during the scramble, hid until the marines turned up, maybe turned into an ordinary marine later, gotten on to a ship, and voila, he's out.
Fan-fic? Sure, 'cause it's not cannon--but this or something similar is definitely possible, given Bon's DF power and the fact that BB was still in ID creating havoc after Luffy left.
I don't think your idea about Magellan could work because he ended up in the hospital after BB was through with him–but if Bon didn't escape I suppose it could be a theory. Problem is, he'd soon find out Bon knows nothing about Luffy or the escaped prisoners, and that'd be the end of that.
I do not personally believe that Bon-chan is dead, and I wouldn't be at all surprised if we see him turn up again some time.
Gah! I'd completely forgotten about BB still being in there at the time…....idiot
That renders that theory useless then!
I DO like your theory though, I could see Bon slipping away in the confusion, but can't imagine that Magellan would let him get away so easily after being in such close quaters with him.