Tell me if I'm wrong but wasn't malleability known for years and more of an issue with how the programers of certain exchanges verified that a transaction was sent (the lazy way of just checking the transaction hash)?
Yes, malleability was known for years and, in my opinion, wasn't even a "bug." It was just the way bitcoin was. Competent exchanges could never be affected by malleability.
But it seems to me (I should give credit to DeathAndTaxes) that if the ECDSA signatures were not included in the transaction hash, then malleability would have been impossible right from the start. But perhaps I'm missing something and it was important that the signatures were included in the transaction hash.