While not being able to update all students' repositories at once is a limitation of the sandbox approach, having tried to fork and pull request model, the advantages far outweigh the disadvantages. When I've run into this challenge, it has been for new code as opposed to changes to existing code. I have opted to post the code on Canvas (our Learning Management System) and have students add the files to their repositories manually.
There is probably some way to automate via a script the process of adding files to each student repository given a list of all student repositories. I haven't been inconvenienced enough to do this