It's not difficult at all, when you understand the workflow and are honest with the user about the ramifications. If honesty is difficult, that is the problem.
You still didn't address this? Care to elaborate on what the "honest" path is here?
1) Have one confirmation that explains the situation clearly (≤ 3 bullets) and avoids fat fingers, such as disallow input for three seconds.
Github delete repo flow is reasonably similar.