Hi
I'm sorry to hear you might have Marek's in your flock, it is a horrible disease! I've had it for 3 years now and whilst there has been some heartbreak, it has not been as bad as many of the stories I have read of others experience.
I would separate the two cockerels now, particularly if you don't have any older hens to put them in their place. Those boys are going to hit puberty very soon and with their raging hormones, they will start to terrorise the pullets, who take longer to reach sexual maturity. The stress of being chased and terrorised by rampant cockerels trying to mate them when they are not ready is one of the things that I have found triggers a Marek's attack. Keeping the flock as happy and stress free as possible and good nutrition to support the immune system are two of the most important factors with Marek's in my experience. That said, the cockerels may get stressed at being separated from the girls, but when you have seen them raping and pillaging the pullets for a few days and perhaps the pullets starting to suffer paralysis from Marek's as a result, it is not something you worry so much about.
You would have been better off getting an older established rooster who was perhaps being replaced in a breeder flock as he would have been easier on your pullets. Juvenile cockerels are a pain, especially when there are no older hens or a rooster to teach them some manners and respect.
If you have Marek's in the flock, then you need to consider where you are intending to go with your breeding program, because selling youngsters is almost certainly going to pass the disease on to others.
Good luck with your flock and I hpe it turns out to be an isolated incident.
Regards
Barbara