I know now we cannot delete Sales Invoice, Stock Reconciliation, and other stock related entries. But as admin if we navigate to the linked Stock Ledger Entries and delete them, anything can still be deleted. 
Will this mess up something though? and how to fix that mess? 
Your answer is in your question itself.
Even as admin, shouldnt the system prevent an action that could affect the integrity of stock? (which I am not sure it would and I want to know if it would. If yes, any possible ways to fix that?).
I messed around and Canceled a Stock Ledger Entry. Wasn’t able to amend it (amended_from field missing). Then I deleted it. and deleted many others. 