Any exposure to the feather dander could potentially expose them to the Mareks virus. The chicks must have 2 weeks of no exposure after vaccination to protect the chicks. Are you planning to raise the chicks in a brooder away from the broody hen? I would agree that if the broody hen is sitting on the eggs, and she hatches them, it is too late. But you could try this since you have already spent all of the money on getting the vaccine. Or keep the vaccine refrigerated fo another incubator hatch later.
I really feel bad for you dealing with this. I prefer to let a hen raise her own chicks around the others in the flock. Those chicks tend to do very well later. There are a lot of different opinions about raising chickens with a Mareks positive flock. Some never ever vaccinate, preferring to know when a chicken has Mareks, so they can cull them. I do recommend vaccination, but only if it is given at the hatcheries. Unfortunately, vaccinated chicks can still succumb to the disease, but I prefer giving them a chance.