Auto-scaling, how to securely get code from private repo
Option 1:
You could place your private repo in the same VPC as the instance and then pull code from there. Just make sure the repo cannot be accessed from outside the VPC.

Option 2:
Ssh into the new instance and SCP the binary over.

Option 3:
Use docker and deploy a private container registry (e.g. Amazon ECR). Build the image on your machine / build server and then push it to the registry from where it is available to your instances to pull and execute.