Firmly agree with other posters that Microsoft's identity services leave a lot to be desired... but Jeff is being a bit sensationalist here.
The school did not "take over" his MS account. At some point (likely amidst a mountain of other onboarding tasks for his daughter's enrollment) he would have received an invitation to join the school's Azure AD tenant as a guest/external user. In this case, he chose to join using his Microsoft account, rather than create a new email-based guest account.
"Leaving" the school's org only breaks one side of the federation, and the guest account and it's association to the school's Azure tenant still remains.
To resolve, he'll need contact the school and have them delete the account. Meanwhile, it probably would have been better to create the app beneath an Azure AD tenant belonging to the non-profit org in the first place.