The penguin was going to be killer whale munchie had he not found the boat. The pod was hot on his trail. He must have been terrified, and chose what he hoped was the lesser of two evils.
When an old friend worked at Palmer Station years ago he said he watched killer whales bump small ice bergs to knock the penguins into the water so they could eat them It is a wonder they didn't do this to the Zodiac. Maybe they just knew there were bigger benevolent "penguins" in there, too.