As I understand your comment, the thing here is that this is not primarily a technical problem. The primary problem (or perhaps it's better to call it a task) is psychological. There are, as has been pointed out, several ways of solving the problem technically, with various sets of of pros and cons. Your suggested way, deleting and re-forking on Github, may not be the most elegant from a technical point of view, but I think it's the best from a psychological angle. I started out looking at this with my work eyes, where "never lose information!" is a high priority. But that's not relevant here. Here, it's a question of letting a user go "toss this mess and start over". From that point of view, nuke-and-refork is clearly superior to at least my suggested way of juggling branches. Partly because it's a more robust way of getting out of any possible git problem, but also -- and more importantly -- because it's a lot easier to understand, and that's important for a user who's feeling unsure. You can explain it in one short sentence ("We remove EVERYTHING and start over"). My method? Not so much with that, no.

Also, given this, I think that just having one script is the better choice. With the goal of making an unsure user feel safe(r), fewer options is better.