I think one approach to this topic is one of scale and application. In this view, childhood is a kind of slavery (and hence a kind of necessary evil). The foundation for this point of view is two-fold; there is some responsibility on the part of parents to train children so that they become mature, and as you point out, the application of apparently initiated force of the parents is apparently effective and desirable, and secondly there is no human agent better suited, on a societal level, to intervene on behalf of children for the "abuse" they receive. The second point requires elaboration: That is to say, the undesirable consequences of invoking societal structures to protect children from the small number of parents who are not fit outweigh the negative consequences such enforcement entails. This last point is also questionable. It's probably not questionable if the societal structure is general, as in "child protective services of government." If, however, the societal structure involved is voluntary, like some kind of "church" or something, or maybe even family, then I think one could get some decent "worst case" outcomes.
In any case, I don't think it's difficult to isolate a structure like the family, which is responsible for parenting from the general tenets of the non-aggression principle as applied between unrelated adults. In summary, the non-aggression principle simply is limited in application.
A second approach is the one you've hinted at below, though it's a little weird. In our current society, there are structures that can penalize you for being "negligent" as a parent based on some basically arbitrary government standards. In the presence of this undesirable societal structure, a child can act in a way that might be interpreted as aggression against the parents---because of the consequences that action might cause. I guess this could be used to justify spanking as self-defense. That seems like a bit of a stretch, however.
The dilemma is a real one, I think (at least in the minds of libertarian leaning parents). And thinking about the non-aggression principle has certainly effected my parenting. I would add, however, that some level of spanking and other punishments as a means to bring about maturity---at least in certain circumstances---seems to produce much better results than the approach of foregoing punishments out of (what I would interpret as) apathy. In addition, the level I have used seems to have been negligible in reducing an appreciation for non-aggression and liberty. Most of my children are far more insightful on these topics than I am. There very well may be superior methods which include a consistent application of the non-aggression principle, but I haven't seen them.
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