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But that punishment-reward thing can easly fit into manipulation.
Well let me turn that around on you - why do you assume that a healthy relationship contains no manipulation whatsoever? I think that this is correct in no relationship ever, but more often women are the party who use it most. Sex as a weapon ect ect
Also, you may share similar views on many things, but you would be remarkably bored if you were a carbon copy of each yourself as a LTR - and I would expect the closest you'd get to be a sibling (stemming itself from manipulation on your behavioural patterns by your parents). Having differences is a good thing - making a big deal out of them is perhaps not.
The fact that you let her know you can end the relationship if she does not suit your lifestyle (directly or indirectly) is in itself a form of manipulation.
I think "control" and "manipulation" may be what needs to be seperated. I think control is a large cause for the breakdown of relations, when a couple loses their equality balance. It becomes a psychological metagame war whereby you know how she thinks and can use that against her, but she knows that you know this and will try to throw curve balls, but if you're aware of her knowledge you can sidestep and have the upper hand in a relationship. It probably comes from us as humans being so emotional - in the moment we do not use logic and instead will find anyway to backward-rationalise why we are in the right. There is no need to always be in the right.
The punishment/reward system is a form of Operant conditioning. You are aiming to have good behaviour repeated - possibly in the future without the need to reward that behaviour.
http://en.wikipedia.org/wiki/Operant_conditioning