A lot of the choices came off as arbitrary because you didn't know how the plot would end up to begin with. Sure, you know Ciri was going to be central to it, but did you know your parenting choices would have an effect on whether she "dies"? No, you don't, and the game doesn't tell you, so when it offers you those parenting choices, you have no idea whether it's just fluff content vs. vital C&C.
And I'd argue that it isn't just a matter of being overly protective. For example, I distinctly remember the scene at Avallach's lab - and keep in mind Avallach is presented as a wise, heroic character in this game - where Ciri wants to SMASH, and you have the choice to either tell her to man up to her destiny, or "go ahead, do it." I'm sorry, but which parent would actually take the second choice and think it'd be a great way to raise their child? That whenever they want to throw a tantrum, you just let them?
In fact, a lot of the parent-child interactions between Geralt and Ciri feel retarded, even in retrospect. Think about the "correct" choices in 2/5 critical events: "hey I know, SNOWBALL FIGHT!!!" in Blood on the Battlefield and "go ahead, SMASH the lab cause you feel insecure!" in Child of the Elder Blood. In these two cases, Geralt is basically treating Ciri as a child, yet they're the "correct" choices.
The other three are less problematic because two of them are straight-forwardly "are you a douche?" choices: ie do you accept money in front of Ciri's face for retrieving her, and do you forbid Ciri to visit her friend's grave for no cause besides "I'm in a hurry." The third one, where you allow Ciri to face the Lodge alone, is capable of being portrayed as not being overly protective, which is fine.
But then where does that leave us? Two "douche" choices, one "overly protective" choice, and two "be a child" choices? Not exactly impressive in terms of the moral it teaches.