I would do it but watch for a few things. Let's discuss Marek's first. The Marek's vaccine is actually Turkey Marek's. It does not prevent Chicken Marek's but does prevent the lesions from forming. The lesions are what does the damage with Marek's. Either flock may have Marek's and not show symptoms. It s possible one flock may infect the other with Marek's. But the odds of that happening are absolutely no different because of the vaccination. The Marek's vaccination is not a factor in the decision. Turkey Marek's will not hurt your chickens.
The cocci vaccination is fairly new. I'm not a medical professional and do not claim to be an expert, so don't trust me totally. There may be different versions of the vaccination but I'll tell you a bit of what I understand about the one I am aware of. I believe there are seven identified different protazoa that cause cocci. The vaccine I am familiar with protects against three of the seven and provides absolutely no protection against the other four. My understanding is that the chicks are infected with weakened versions of the three protazoa so they can build up an immunity to those specific ones. It does not mean that the chickens cannot carry those specific protazoa. It just means that those specific protazoa do not harm that vaccinated chicken. Whether the vaccination makes the vaccinated chicken a carrier for those specific protazoa, I do not know.
I would merge the flocks, after the appropriate quarantine, and watch for signs of cocci. If cocci shows up, since you are on the watch for it and the symptoms, you can catch it early and treat if it does show up. The non-vaccinated birds may give the vaccinated birds a version of cocci they are not protected against so it could be either flock infecting the other.
Relative to your question, the main difference between Marek's and cocci vaccinations is that I know the Marek's vaccination does not make them carriers of Marek's. I don't know whether or not the cocci vaccination makes them carriers of the version of cocci they have been vaccinated against.
There are other vaccinations available besides Marek's and cocci. One of them, I believe it is for Laryngotracheitis, makes the bird a carrier and it will infect other chickens. This is the only vaccination I would worry about and it is seldom given.
Hope this helps some.