Users that are capable of diagnosing what went wrong with their repo are also comfortable setting username/email in the config.
For the rest of us, having a pretty UI helps. And I don't see how is being user friendly and offering to just do it can ever be a bad thing. Especially when the alternative is forcing people to figure out how a config file works. Should it be in ~/.gitconfiguration? ~/.gitconfig? Whats that . mean? That ~? A typo'd and it gets made it in ~/.gticonfig..
I have some stuff in my gitconfig that I like having, but, would never be able to figure it out if someone didn't A. tell me what to do or B. make a script that did it for me. And no, I didn't enjoy reading dozens of git manpages to try and find what I wanted. It really sucked.
If the user doesn't think something is odd when the program wants initial setup info again, there's no helping them either way.