I'll just play devil's advocate and say that Neji didn't have any intention of seriously hurting or injuring Naruto at that point. His intention was simply to humiliate Naruto so he sealed of his chakra points and announced that the match was over because Naruto couldn't use his chakra anymore which was the truth. It was after that, when Naruto gave his BS speech that Neji said he was going to kill him and even then he wasn't serious.
We saw already in the match with Hinata that if Neji so wished he could seal of someones points with such a gentle touch that even another Byakugan user wouldn't notice. So I'm pretty sure that the amount of damage the technique does is completely up to Neji. Besides I thought the strength of the gentle fist as opposed to the iron fist or whatever it was they called it was that the gentle fist could kill without requiring any substantial amount of force to be used and without causing external damage. Even if Neji was training to increase the amount of damage he could do in the same amount of time it would make sense that he would increase the amount of damage done by each hit rather than increase the number of hits themselves, for example when Oro invaded the village we saw Hinata's father killing people with one hit and as we saw with Kidomaru Neji can kill with the 64 palm.
Anyway like I said I'm just playing devil's advocate, for lack of anything else to do.
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