Yeah, it's unclear to me at the time if the dialogue box in the screenshot appeared when doing a select all operation, but it reads as though the OP dev didn't understand git, discarded their work, and got upset that it was an option.

Realistically if the dialogue box appeared, I'm not sure there would be anything else the IDE could do to prevent the dev from themselves. Perhaps reject operations affecting 5000 files? But then you'll just have someone with the same issue for 4000 files.