It's always best to quarantine new birds as far away as possible from the existing flock for 6 weeks. Some diseases can go airborne, others transmitted on clothes, shoes etc...Some diseases have longer incubation times than others. That's why 6 weeks is best for quarantining and it'll give you time to watch for illnesses to show themselves as well as inspecting him for abnormaties, parasites and so on.
I'd seperate your rooster and hope for the best, and watch your existing birds for any signs of respiratory diseases or anything out of the ordinary. There are some diseases that are transmitted through sharing feeders/waterers with other birds. If this didnt occur in your instance with your rooster, perhaps everything might turn out just fine...time will tell.
