First of all, kudos to you for trying to help these poor animals! It sounds like they were living in abhorrent conditions.
When I rescued two roosters someone abandoned on the highway, I put them in quarantine and then wasn't sure what to do with them. I wasn't prepared for them at all, but couldn't leave them starving and scared on the highway. I talked to a vet who said to test them for worms, coccidiosis, and Mycoplasma gallisepticum. We never did test them for Mg because we decided we were going to keep them anyway (I also was lucky they showed no symptoms of illness, although that doesn't mean they're not sick). I quarantined the birds for a couple of months to make sure they didn't show signs of illness. Again, no guarantee they're not carriers of something, but it's one of those decisions we all have to make when we pick up rescue birds - kill them or take a chance. We took a chance, and luckily, we haven't had problems so far.
Before making my final decision on keeping or killing the roosters, I contacted a poultry sanctuary for advice at United Poultry Concerns. Pyxis is right that it is incredibly risky to take these birds in, but sanctuaries do deal with these things all the time. If I were in your position, I would contact this sanctuary (or others) and see how they deal with new birds that are sick. You may still decide to kill them, but at least you've talked to someone who has devoted their life to saving rescue animals and has surely come across this problem. Here is the contact info for the one I contacted:
[email protected]
757-678-7875
The woman there responded very quickly and is very helpful. She has run this sanctuary for years and has a lot of experience.
If you do decide to keep them, make sure to give them a good physical - check closely for mites and lice if you haven't already done so.