Basically, you aren't supposed to be able to delete sections, because sections provide the context for a lot of essential data in SchoolTool.
A lot of the inconsistencies you're experiencing is because you were determined enough to kill your sections, which nobody had really tried to do before. So we either need to make it even more impossible to delete sections, or recover more gracefully when the go away.
Basically, you aren't supposed to be able to delete sections, because sections provide the context for a lot of essential data in SchoolTool.
A lot of the inconsistencies you're experiencing is because you were determined enough to kill your sections, which nobody had really tried to do before. So we either need to make it even more impossible to delete sections, or recover more gracefully when the go away.