I don't understand what you just "proved". You conceded that knew your machine was in an unhealthy state, and you claimed that stressing that state resulted in a system crash. OK, fine, whatever. How do you draw the conclusion that the OS being dependent on a certain data store is "bad design"?
Before you answer, yes, Microsoft does happily admit that mucking about in the registry may cause serious issues. Any KB article that references registry keys carries this warning. This is clearly "by design". But why whould this be a "bad design"? What would be a "good design" (that doesn't also stop a legitimate owner of the machine from configuring the system however they seem fit)?
