I imagine that Magellan's defeat of the BB crew was meant to make us underestimate BB, and at the same time add to the mystery of him. It did come out of nowhere after all. Who expected the guy who beat a Whitebeard Commander to be beaten in one panel. I didn't, and frankly it still doesn't seem legit to me. I mean, some of those guys could dodge Ace's fire attacks but not Magellan's poison? Weird.
In fact, that's the only thing I don't like about Magellan. He's this huge powerful guy who came out of nowhere. He's about as strong as any of the shichibukai, or at least his ability makes him that strong to certain people. Then again, Croc and Jimbei didn't seem to have the confidence to defeat him, so maybe I wouldn't be wrong to say that. He's like this "fake shichibukai." Oda needed someone as strong as these guys but couldn't have one of them fight here, so he made this guy up. That bugs me, though I'd personally be satisfied to see his story get resolved.
That aside, despite a loss Blackbeard could do anything he wants the next time he shows up. After all, by that time he'll have finished whatever he was attempting to do at Impel Down.