He ducked, if only because the order was a wise one to follow, but it really wasn't nessacary. These older guns just did not hold the power needed to travel all the way through one body and into the next. It was why Haytham so often found himself using enemies as human shields. Using an ally as one however... It was not planned for and brought several emotions to the fore that had to be ignored if they were to get out of this alive.
Hands fell on her shoulders to support her as soon as it had been made clear just what had happened.

"Now we really must leave."

She couldn't be expected to carry on the fight like this. It was his turn for a little trick then. She had used a vile of acid to distract and injure the crew and he had something similiar. A smoke bomb was drawn from a pocket and tossed down on the deck. It did no harm to the men close to it but the thick smoke did make it difficult to see. The crew found themselves once again reeling from a surprise attack as they choked on the smoke and were blinded effectively enough so that the pair could make their way up and over the rail of the ship. The seaman heard the splash when it came but could do nothing about it.