My Son Has A Compromised GI System With Food Allergies

My son has a compromised GI system with food allergies and constipation issues. I keep him away from antibiotics religiously. He is 4, he was diagnosed with strep throat this Monday from a Dr visit last Friday. He is feeling better today, no fever, he is playing and eating. I don't want to put him on antibiotics. I feel it will compromise his gut even more. I feel the antibiotics are a greater danger than the incredibly small chance he will get rheumatic fever. However I understand rheumatic fever can damage his heart and have life long complications. I don't know what to do. Please help! I hate both options here.