If this were my game and the players seemed set to bring their followers into battle, I would let them.
On the boat trip towards their destination, I would have some monsters attack. Maybe level 5, but with jacked up attack bonuses so that they could hit the PCs. A whole bunch attack at once, enough to tax the PCs and force them to scramble around to protect the followers, but not enough to really pose a threat to the PCs. The challenge of the encounter would be to fight off the monsters (who can damage the PCs, but are utterly lethal to the followers) while keeping casualties at a minimum.
That would be their warning. Taking followers into your battles will end with dead followers! If they ignore the warning and take the poor slobs into the adventure proper, that's their choice. I wouldn't really change the way I design the adventure at all, which means a lot of the little guys will die, which means you won't have to deal with the issue for very long.
Of course leaving the followers elsewhere while the PCs (and cohorts) do the real work is more manageable, and it sounds like you have that well in hand.