That's not how it works, really. The vaccines that we have used on a global scale likely gave the hotter strain a place to develop, yes. But the vaccine still works against the hotter strain. The vaccine still works against mutated strains of the virus. And the chances of your flock suddenly developing an even more hotter strain of the virus that breaks through the vaccine is infinitesimal. Those kinds of mutations take many decades over the course of billions of birds. The mutation we have now doesn't even break through and we've been using the turkey vaccine for a good 70 years.
And in any case. If your chickens aren't vaccinated against Mareks and are exposed to Mareks, they're pretty much all dead anyhow. It's just that you know you have Mareks and what caused the deaths.
The vaccine itself does not effect meat quality. Neither does the virus, except organ quality. The vaccine goes through the body fairly quickly and there is no meat withdrawal period for the Mareks vaccine. Mareks is a species-specific virus, not a bacteria so there's no real risk associated with getting a low dose of the vaccine in your food.
Also, a vaccinated bird can't just "have" Mareks unless it's exposed to Mareks. The Vaccine isn't even made with chicken Mareks, it's made with the much less deadly turkey Mareks which chickens cannot catch.
The only thing that will give your chickens Mareks is another bird in the area that has Mareks shedding the virus in a place it can be carried back to your birds. (This can happen even on shoes or clothing, so practice good biosecurity first.)
If that happens, and your chickens are unvaccinated, you'll have massive losses. But you'll know you have Mareks. If that happens and they are vaccinated, they will live but you may never know you have Mareks. If that happens and your flock is mixed, your vaccinated birds will be fine and the unvaccinated ones will have massive losses and if you have a fair number of bird you're very likely to know it's Mareks. Either way you will have Mareks in the soil for the next 3-10 years.
If that never happens there is no difference between vaccinated and unvaccinated birds.
Whichever option is right for you depends on your goals. If it's more important to KNOW you have Mareks then it is to keep your birds alive, don't vaccinate. If it's the other way around, do.
(For reference, my birds are unvaccinated and I don't think people should. I think people should cull their flock if they have Mareks. I just want to make sure you understand what the real situation is without fear mongering.)