Pruning can be good and pruning can be bad. It depends on a number of factors. Proper pruning should start early in the trees life and should be done sparingly. It does say in Proverbs 22:6 that you should train up a tree in the way it should grow and it will not depart from it when it is old (unless a big ice storm comes along). I may be paraphrasing, but I remember it saying something like that.
Pruning to develop a good structure is a great thing to do. The tree will have that same basic structure for the rest of its life, which may be well beyond yours.