One problem you did not mention is that escaped farmed salmon, which have been selectively bred to be fatter, have interbred with wild salmon. The resultant offspring are not strong enough to migrate and therefore do not breed. This is one of the reasons for the decline in the numbers of wild salmon.
You point out that antibiotics are used to stop the spread of disease in the overcrowded fish cages. This applies to other forms of intensive farming too: nearly all pigs, cows and chickens reared for meat are given antibiotics every day in their feed. The resultant increase in the resistance of bacteria to antibiotics is already affecting our ability to treat human illness.