I think the banking regulator and or justice system in the relevant country step in. Being in a modern society with laws seems to be the main, partly effective preventative measure. If we're going through the work to have laws and courts and regulatory bodies anyway, and if we have the FDIC etc, why shouldn't we get a partly-trustworthy financial system out of it? I mean, of course, not that the people are trustworthy, but that records of what you deposited, withdrew, transferred etc will be respected.

Even if you own crypto, I'm guessing you have a bunch of money in other assets in accounts managed by financial institutions. How often has the bank just decided that you don't own that?