While git is indeed a usability clusterbomb and there is massive space to improve, the problem above sounds like a devops failure. Git gives you all the tools to prevent such a disaster, all you have to do not give the root password of your CI server to any data scientist.
On the topic of your startup, I would very much like a lighter learning slope, where I can introduce regular non-coders to the benefits of source control, and still have the advanced brancing/merging/rebasing etc. for the wizards.