Help with kraken

A few moments ago, while doing a Grade V Athena Emissary Quest, our galleon encountered a skeleton ship, a Kraken and then the storm came upon us.
We were actually handling it pretty well, when the kraken blocked the entrance. We were all below deck so we could repair and bail out water, except the tentacle was blocking off the only way we could throw the water out. We had no time to shoot it enough times to repel it.
Meanwhile the skeleton ship was shooting limpballs and ballastball.
I think such scenarios shouldn't really exist, but they do so I'm not here to complain. What could have we done to survive in this situation?