As Terry says, it's supposed to be "had his will": it was mistakenly (or in fun?) changed to "hold the wheel" for a period in one community, then that error perpetuated among revival singers -- here's the quote with italics:
"On Cyril's first recording of the song, made by the BBC (Child Ballads Vol I, Topic 12T160, 1961 [originally Caedmon]), singer and audience constantly interject the phrase hold the wheel. This allegedly arose as a result of the singer trying to explain the story to a visiting yachtsman who misunderstood had his way as hold the wheel, but by the 1970s Cyril had gone back to the old way of singing it."