You'd have an argument if, and only if, the ability to control Big Daddies involved the story in any way. Hint: It doesn't.
It's sort of like saying Kratos eventually gains the ability to cast spells, but you'll probably never use them. It's simply an exposition of the gameplay rather than anything involving the story.
Now, if I told you why you gain Control Big Daddy then that'd be a spoiler.
To be fair: They're surrounded by the criminally insane and have fallible defense systems. There is little to no reason not to want to save them.