At the Risk of Sounding Like a Broken Record...
Pielorinho has got the right idea...
The players got the drop on the Theocracy (and the DM), used creative tactics and overcame a superior foe. A moment of sweet victory to be savored...for about five minutes
!
I suggest:
(1) The Theocracy has been embarrassed and bested by arcane magic wielders. They are going to be pissed in a very holy way.
(2) Clerics excel at divination...the Theocracy is going to find out who, what, when, where, how and why this upstart band attacked one of their ships and triumphed. When they find out that arcane magic users are part of the enemy, they might launch a mini-crusade after the party.
(3) As others have suggested, pick up Mongoose's Seas of Blood...it has some good ideas on ship defenses. I would also submit the a kingdom of sea-faring clerics would have developed significant protectives and counter-measures against normal attacks (fire, acid, warp wood, etc).
(4) If the Theocracy is allied with any druids, a mid-level druid or two in the shape of a dire shark might be a small deterrant against swimming rogues.
(5) Although the Theocracy as a whole hates arcane magic, there might be a few pragmatic leaders who would offer a letter of marque to hunt the "vicious pirates" (ie, PCs) to aspiring privateers, not really caring what means are used to achieve the end.
(6) Finally, you have a fine opportunity to set the Theocracy up as as a long-term, intelligent nemesis. Use the inherent strength of clerics - protectives and information gathering - to make sure the next encounter happens on the Theocracy's terms.
My 2 coppers...
~ Old One
Pielorinho has got the right idea...
The players got the drop on the Theocracy (and the DM), used creative tactics and overcame a superior foe. A moment of sweet victory to be savored...for about five minutes

I suggest:
(1) The Theocracy has been embarrassed and bested by arcane magic wielders. They are going to be pissed in a very holy way.
(2) Clerics excel at divination...the Theocracy is going to find out who, what, when, where, how and why this upstart band attacked one of their ships and triumphed. When they find out that arcane magic users are part of the enemy, they might launch a mini-crusade after the party.
(3) As others have suggested, pick up Mongoose's Seas of Blood...it has some good ideas on ship defenses. I would also submit the a kingdom of sea-faring clerics would have developed significant protectives and counter-measures against normal attacks (fire, acid, warp wood, etc).
(4) If the Theocracy is allied with any druids, a mid-level druid or two in the shape of a dire shark might be a small deterrant against swimming rogues.
(5) Although the Theocracy as a whole hates arcane magic, there might be a few pragmatic leaders who would offer a letter of marque to hunt the "vicious pirates" (ie, PCs) to aspiring privateers, not really caring what means are used to achieve the end.
(6) Finally, you have a fine opportunity to set the Theocracy up as as a long-term, intelligent nemesis. Use the inherent strength of clerics - protectives and information gathering - to make sure the next encounter happens on the Theocracy's terms.
My 2 coppers...
~ Old One