This is just an idea. What about a new building (i.e. Guard Tower) where you could place your recruited troops? They would be deployed if the enemy attacker comes close to the building. Then, they would have the same abilities as if attacking another island, just that they would be attacking an enemy pirate instead. Their special abilities would... er... be cancelled. (What use is a "Bring it on" to a defender?) Just an idea, but maybe Chris[Midoki] could give it a thought. The pirates would die when all their health is gone too. Just one flaw: Thieves would have to attack other pirates too instead of attacking stores.
I don't think this would work well in this game. Bases are hard enough without pirates defending them.
I have a similar idea but without the new building. Use the Guild Ship, as it is the counterpart of Clan Castle in COC. Also add a different music while they march out.