tx malleability was never a bug, just a design compromise, with risks, which needed to be worked around when building exchange (and similar) systems. However, core dev have recently made a few improvements which makes containing the risks easier. All the other exchanges are fully aware of it and done necessary changes. Kraken for one did not need any changes.

MtGox's problem stems from being the first exchange and making an early custom copy of the software, not properly coping with tx malleability, maybe because their business grew so fast they were distracted by performance issues, and negligent in maintaining certain other areas of their system.