Pruning
The main reason for pruning is that it helps to develop the growing branches, allowing you to directly control the shape of the plant. Each time you clip off a growing tip, two new tips start developing from the nearest leaf axil. By pruning the tips of the upper branches, you also give the lower branches a little time to catch up. When the lower branches catch up, the plant forms a flatter top and the light is able to reach more growing tips.
The occasional clipping of a growing tip will not seriously affect the growth or health of the plant, providing you don't repeat this too often, or clip of more than just the top two leaves. The clipped branches always require a few days to repair the damage before resuming vegetative growth, so you shouldn't clip them again within a week or so of the previous clipping. Seedlings should also not be pruned, allowing them a little time to build up the energy required for repairing plant tissue.