A good rooster should never bother chicks. Sometimes a rooster will even adopt them or help a broody hen take care of her chicks. So yes, I can see why the chicks aren't afraid of him. Most hens aren't that dangerous either but they are more dangerous than the rooster. Occasionally you get a hen that will out and out attack the chicks. What often happens is that the chicks invade the personal space of a mature hen. She doesn't like it and will peck them to teach them that it is not polite for them to bother their social betters. She might chase them away but often it's just a peck. The chicks learn really quickly to avoid those mean old hens. Hopefully that explains a lot of their behavior.
When might you see a cockerel clash with a mature rooster? That is hard to answer. He may hit puberty in a couple of weeks, it may still be months away. Typically my roosters don't bother the cockerels until much later but I may have more room than you do. What I normally see is that the cockerels are interested in pullets their own age at first. Your pullets are a couple of weeks older, that might add some twists to it. But as long as the cockerels leave the adult hens alone my roosters aren't that bothered. When the cockerels start bothering the mature hens the mature rooster gets involved.
My immature chickens typically stay a long way away from the adults. It's possible your rooster will object to that cockerel trying to mate the pullets in his presence if they are closer.
Until the cockerel reaches a certain stage of maturity he will not challenge the rooster. He will run away. Cockerels mature at greatly different rates. Typically that's around seven months for mine but it can be a couple of months earlier or months later.
Is it possible they will coexist peacefully? With living animals anything is possible and that actually happens quite often, especially if they are raised together either as siblings or father-son as yours are. A lot depends on the personalities of the individuals and how much room they have. They will know which one is boss. That may involve fighting, it may involve chasing and running away. It could be really violent, it's possible you won't even notice. My main suggestion with that is to have a plan so you can isolate them from each other at a moments notice because the need may happen that quickly. Or the need may never arise.
At nine weeks if you can post a photo of the head showing the comb and wattles development and color, and a separate photo showing the legs, posture, and body profile we should be able to make a real good guess the sex of a Marans. Maybe we could help you relax or get your plan together.
