An interesting one, and quite unusual in my experience. It is much more common for brides and grooms from complicated families to "normalise" their birth relationships on marriage certificates (by naming fictitious fathers when their own was unknown etc).
You say that you *know* that Ellen/Eleanor was the daughter of John and Eleanor - do you have a baptism record? Was she baptised as an infant? Were there other children? When did John and Eleanor marry?
The most likely scenario is that Ellen/Eleanor was the illegitimate child of Eleanor and William and that all concerned were aware of this, despite Eleanor's subsequent marriage to John.
More questions than answers, I am afraid!