You can find all-cotton non-flame-retardant jammies at Carter's. That's where I have bought all of dd's jammies. Since 6 months old, she has worn their 2-piece sets.
I'm not completely sure about this, but I think that the pajamas only need to have the flame-retardant chemical in them if they are not made to be snug-fitting. If they are snug-fitting, they do not require the chemical, because there is no loose fabric.
All the cotton pajamas I buy at Carter's are very snug-fitting (like long-johns). Their flame-retardant pajamas are all looser.