How can I remove GPG-AGENT setting from Enigmail?
I don't use macs, nor do I know if this will work for you, but I came across this question when searching for why I don't get a passphrase prompt.

Take a look at Thunderbird Preferences -> Advanced page -> General tab -> Bottom-right 'Config Editor...' button to get to the usual Mozilla about:config dialog, then search on extensions.enigmail.useGpgAgent.