Complex sentence: Half of his crew went ashore to say prayers in a chapel to give thanks for having survived the storm, but while praying, these crew members were imprisoned by the island captain, ostensibly on suspicion of being pirates.
Split into simpler sentences: Half of his crew went ashore to say prayers in a chapel to give thanks for having survived the storm. But while praying, they were imprisoned by the governor of the island, ostensibly on suspicion of being pirates.