The article doesn't make clear what sort of hooks and line these were. It's likely to have been a big, heavy, motorized rig from which the line and hooks couldn't be neatly separated, especially while frantically aligning the boat and bailing water in a freak storm.
We should also bear in mind that, at that moment, Alvarenga wasn't anticipating a year at sea. In fact, he was acting to prevent that fate. He believed that his first priority was the right the ship at any cost, because the alternative was capsizing or going adrift. From there, he'd planned to make it back to shore or be rescued in relatively short order.
It's too easy to critique his choices retrospectively. Some of them look bad on paper, out of context. But I've never been placed into that sort of context.
As a general rule, your first priority in any emergency at sea is to stay afloat. This directive overrules all others until you believe your vessel is stable and secure.
