Haki vs.Venom Venom Fruit
No, Haki wouldn't help him.  It was established that many prisoners knew how to use Haki and that Magellan was the only one capable of keeping them in line.  Furthermore Blackbeard and his crew are potent haki users, he definitely got his butt handed to him only to be saved with the antidote from Shiryu.  

Its good to note that while haki lets you hit the body of users, it doesn't negate powers like the sea, or yami yami fruit.  While the Haki user can hit Magellan which was never an issue for Luffy, it poisons anyone who has contact with it.  

Similar issues are present with some other paramacia users like Sugar in the Donquixote Pirates where contact with her turns even haki users to toys.