I think I wouldn't be surprised if the Bitcoin devs face a lawsuit eventually as a result for knowing about the transaction malleability issue for about 3 years and not making a serious effort to address it.
I believe transaction malleability is not a bug; it's just a result of how the protocol works.
You may want to change and resubmit a transaction that failed to go through.
It's a case of.... blame the protocol for implementation errors in your automated system.
It would be kind of like cashing a check.... and immediately crediting the user with tangible goods.
Without accounting for the possibility of the check bouncing later, or failing to clear due to error nonexistent account or stop-payment.
Just like banks have their rules, Bitcoin protocol has its rules.
Businesses that transact, need to understand the rules, and take especial care to protect themselves given the rules, or else, someone will eventually exploit their business.