6 Man Rocks quoted the black letter rule that applies. In practice, it's sometimes difficult to draw the line between when a player is still fighting for yardage and when they have been wrapped up. From your original post, it sounds like you are strong on the situation being one where the ball carrier was definitely stopped and therefore defenseless. When in doubt, officials are going to err on the side of being slow on the whistle and letting the kid continue to fight for yards. Doesn't mean they were right or wrong in this case and you are a far better judge being the one to see it with your own eyes, definitely not going to cast judgment either way!
If he was defenseless as stated, and an opponent made forcible contact to his head/neck area with an indicator, you would have a foul for 9-1-4 Targeting. If he was completely held up and play was over, you could have a Personal Foul for Late Hit or Unnecessary Roughness as well, even without a head/neck hit.
I hate to say "depends," but...well...it depends.
Above anything and everything, I hope the player recovers fully and quickly.