I think what you want to do is make sure that you can ssh (or git clone) from the machine (in this EC2 machine) to git so that github's public key certificate can be added to the known_hosts file of your "deploy" user (the user that capistrano runs as on EC2 machine) so that EC2 machine to Github connection is a trusted connection. I had no ends of trouble because of this since I forgot to do this.
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