I'm not sure that is pecking order. There are three different types of agression I can think of. One is the pecking order. That is the one that really goes on forever, but once it is set, things are pretty peaceful. What I mean by that, as they mature, they will jostle for better positions in the pecking order. But your young ones are at the bottom of the pecking order and will not be doing any challenging for a few months. You'll probably see some stuff as they get close to maturity. Until then, they will run away.
A second aggression is flock dominance. If you have roosters around, this is between roosters, at least if the roosters are mature. An immature rooster and a mature hen may go through this or two hens may do this with an all female flock. It is the one that freaks so many people out. Usually they will settle it without serious injury or bloodshed, but sometimes chickens die while sorting this out. Of course, sometimes chickens die because of pecking order and integration too. But your young ones are too young for this to be coming into play. That won't be an issue for several more months for you.
The third one is integration. This is where a flock does not accept other chickens as part of the flock. They will try to force intruders away from their territory. This might be what is going on. That rooster may be the dominant one and is protecting his flock. Notice I said may. I'm not 100% sure this is what is going on.
It is also possible that he is just a nasty, aggressive, vicious, mean brute. They exist. Often it is a hen but hens don't have a monoploy on that.
Some people will probably post that you have to wait until they are older and all that to integrate them. A hen will often wean her chicks at four weeks and those chicks are integrated in the flock. I personally wait until later, but that is more that I want them bigger before they free range so they are not such good hawk targets. I know. I'm over-protective.
I don't know exactly what I would do in your place. If the young ones are not being injured and they have a safe haven, I'd probably look in on them often but let it go. The danger to me is that one might get trapped in a corner and can't get away. There is a risk. If you have a place you can lock him up but still be with the flock, I'd consider that. The risk with that is if he becomes considered as not part of the flock, he may have to be reintegrated. That's why if you can keep him with them but not with them, it would be best.
I don't know what your goals are. With me, I'd eat that rooster. But that may not be an option for you. And it is still possible another chicken becomes flock master and takes up where he left off. With chicken behaviors, many different things can happen.