Sounds like it's in the mouth as well, that would be wet pox, that I haven't dealt with but know that's a lot worse, I would do a search on this site, there a plenty of old threads that talk about it.
Vaccines can help those that aren't infected avoid getting it. I personally didn't vaccinate because I believe in building a healthy immune system and culling those who can't. I would put your young chicks on antibiotics just to help their immune system along, I wouldn't mess with the sores too much, I believe the scabs can be infectious, so try to minimize handling especially if you also have other poultry to care for.
It does take a while to completely run through and heal, and some of my turkeys eyes swelled shut and I didn't think they had eyes anymore. You could cull, but I would only if they were suffering, otherwise it is already in your environment and getting rid of the chicks I don't think would help you. Good luck.