The attacking of specific chakara sub-points is a very high-level style mastered only by a few. At the lower level, the major chakra coils are attacked directly, resulting in internal organ damage. So even an average user can take down a giant with one hit.
Neji was trying to drive home the point to Hinata that she couldn't ever touch him, which is why he went through the effort of closing the sub-points. When he got pissed off, he just attacked normally to do critical damage. Figure that Neji will usually do normal attacks, as the sub-point technique is really only good for disabling oppenents. Of course, Neji isn't out to kill anyone in the exam (except for that one moment with hinata) so he's more likely to use non-lethal force. And he also gets to show off his mad skill in the process
