the question is who can you possibly trust with something that can be so easily disappeared.
The answer is to never assign trust in a single point. That's the whole reason Bitcoin was designed for, and these thefts really show how backwards we are with regards to the technology we have.
Surprisingly few people actually know this, but Bitcoin addresses are actually little programs that calculate the required criteria to move money out of the "address". It's purposefully Turing incomplete. The simplest defense against malevolent or incompetent parties is to require multiple signatory entities. For instance, one could be the deposit institution itself, another party for dispute resolution (e.g. a lawyer), and finally the customer. You can require only two of three signatures to move the amount so that the customer can extract the money with the help of the arbiter even if the deposit institution disappears.
Other, more sophisticated solutions are also possible, and some of the businesses themselves can even become transparently automated. However, it seems like it won't be that easy to get there, even though the crucial technology is already available.