Repositories are only created when you create assignments on GitHub Classroom. It's at this point that you can use starter code from a repository within your organization, or your personal GitHub Account.
For a student to clone their repository, they can select import project from GitHub, fill out the info and pushes and pulls will go to their repository on GitHub Classroom.
I usually don't find myself using the VCS commands in IntelliJ very often. I use the built in console to do commits, push and pull. I also clone new repos with Git Bash. The only use I get out of it is the merge tool.
I don't think it's unreasonable for even beginner programmers to learn the commands, clone, add, commit, push and pull.