JUST RUN! ignore everyone else, those fighting for you and what not, if you get knocked down, get up and keep going. The enemies are pretty slow at not usually following you to far... at least for me they never did. I only took some damage running past them to the dock. If your using hench, they like to stop and fight... so make sure they keep going with you... you'll need them at the end.
Very strange last night - I tried Sanctum Cay solo a few times and wound up getting annihilated with the last fight. Last night I did it with a guildmate and we only had to fight four guys before the ship appeared. Wonder if that was a glitch?