"She caught up with one of the boats after an hour and the five crewmen surrendered without a struggle. The second boat escaped..." Would anyone have complained about a breach of human rights if they just sank them and been done...?
If you capture the pirates you can get information from them eg where they are based, how many of them, where they get their arms from, is there a mother ship nearby, etc. If you sink them you may well miss out on all of that.
Did you know in the last 5 years there has pirates have killed 65, injured 151 and held 2,000 seamen hostage. Though it all sounds gung ho and swashbuckling it is very serious. Now the Monsoons are over the Somali Coast is expecting an increase.