You
do want to handle your children. You
do want to control them to some degree. You
don't want to use them. I think manipulation in this sense is a neutral enough word to use, and in that light is acceptable. One could argue that the 'threat' (promise or assurance, if 'threat' isn't to your liking) of any sort of negative consequence of an action is in itself manipulation to dissuade one from taking that action.
I think manipulating your children by misleading them or verbally, emotionally, or physically abusing them is wrong. You shouldn't lie to your kids and rule them through fear of you and your responses to what they say or do. It's detrimental to building trust between the two of you.
I think manipulating your children by teaching them that actions have consequences, and helping them to understand what both the actions and the consequences are, and why they exist, and how to avoid both the actions and consequences, is right. You should teach them what is acceptable and what isn't, and lead them through example.
A large portion of how much explaining you can expect to be understandable and retainable by the child depends on their mentality. You can explain a stovetop is hot to a two year old all day and probably not get anywhere, for example. They won't have the cognitive capacity to understand your caring, rational exposition on thermodynamics and the potential damage of heat transfer to the largest human organ. They will likely understand the pain they feel on touching the eye, however, as they will likely understand the pain or discomfort they feel when you slap their hand away from it, or give them a worried or upset tongue-lashing. As they grow older, they will become more capable of understanding and retaining your explanations for why they should avoid certain words and actions, provided they aren't mentally handicapped in some way. They will also become more capable of manipulating you.
Granted, they are children, but this doesn't absolve them from all wrongdoing. It doesn't make them perfect, reasonable little angels. It doesn't make them your equals in every way. And it certainly doesn't make them incapable of being contrary, irrational, selfish punks.
People are not born good or bad, but with the capacity for both, and while environment and treatment play a significant role in how a child develops, it cannot be taken as the end-all be-all of how they will turn out. Kids will do what they want to do no matter what - it's up to you to discern what actions and words you need to guide them into wanting what's best for them. If all you ever need is patience and a gentle or kind but stern word, good for you, but that isn't always enough. Sometimes physical dissuasion is necessary, and just because you personally have never needed it doesn't mean you should go around telling people they are abusive, bad parents, idiots, or morons for using it or condoning it.