Okay, so many scenarios here. Say Cooper isn't Locke's dad, he would've had to hire someone to get random medical files and find himself a match, finds John Locke who has no known parents. Score! So he hires a stranger to pretend to be Locke's mom, etc. But then if Cooper wasn't Locke's real dad I think he'd tell him. He got his kidney, why keep up the con? He was annoyed by Locke and wanted him to leave him alone so why not just tell him, go away I am not your dad. And he tells Sawyer in the brig that Locke is his son. If Locke's mom is Ben's mom then there is no immaculate conception theory because it isn't the same woman who said that.