To be fair to the idea, though, while this would make individual instances less secure, it would drastically decrease the leverage for the work bad actors put in.

There is a saying in the software security industry that (I'm paraphrasing from rusty memories) a system is secure if the cost of hacking it is higher than the value it protects.

Each system being completely distinct from another means that the cost of hacking the average student goes up by 9000 (from the article, Canvas is used by 9000 schools).

Still not saying that rolling out your own is the preferred solution, but the idea is not as ludicrous as it would seem, and should definitely be entertained and discussed, at least.