If you import the rule into the state and it does not match any ressource defined in your configuration, then it logically should be deleted when you next apply the config.
Dunno if Beanstalk recreates it though, only one way of finding out.
Hope this helps, otherwise try and get away from using the default security group.
You mentioned PCI.... If you are not yet in production, I would strongly recommend using the EB stack only as inspiration for writing your own Terraform config that builds the entire solution from scratch. Then you have the full documentation of the solution at hand and that should definitely make your PCI review easier.
Also, take a look at this little utility
https://github.com/basefarm/aws-session-tool which makes it easier to work with cross-account logins using MFA - this was originally developed for a PCI-DSS compliant implementation and passed the review with thumbs up from the QSA.
Regards,
Bent