No need to apologize....you are trying to do your best for the cats, and it is important to say what you feel needs to be said.
I think from what you describe that this is a case of the two of them being playful, while at the same time the older one is making sure (with the neck-scruff holds) that the kitten knows "his place", and that the older cat has seniority and is "in charge". this is normal, and is pretty much to be expected a lot of the time. The senior animal always has to make sure their place in the household is respected, and that's fair enough.
Unless someone is really acting upset by this or getting hurt I would leave them to work it out for themselves. I wouldn't even separate them when the older one is holding the kitten by the scruff. He will let go on his own, and as long as the kitten isn't being hurt it is OK for him to establish order in this way. It is like a mama cat grabbing the kitten by the scruff.