To replace Mary Ellis with a different mother, edit Obadiah's profile and then under Edit Family choose to Edit Mother. A new screen will pop up, which will ask you either to replace mother with an existing wikitree profile or create a new mother.
If Mary was not Obadiah's father's wife, you would need to unlink her from his father as well.
If you know the mother, the replace mother option is the best alternative. You could if you wish, edit Mary Ellis's profile and remove Obadiah as her son, but you would still have to create a new mother for Obadiah.