Here is some information regarding aquaculture and salmon. Certainly this is only a sample of the literature available, but it does provide some insight into the relationship between aquaculture and wild populations. It should also be noted that these are peer-reviewed scientific journals, not publications of political organizations.
Youngson et al. 2001 Genetic interactions between marine finfish species in European aquacullture and wild conspecifics. Journal of Applied Ichtyology 17:153-162.
Paper discusses the escape of Atlantic salmon from aquaculture and mating of those individuals with wild fish, the consequences of such mating events (reduced genetic fitness) for the wild populations and the need to develop policy to prevent problems in Atlantic salmon, sea bass, and bream wild populations.
Heath et al. 2003 Evolution of egg size in captive salmon. Science 299:1738-1740.
Documents the increased presence of a trait for smaller egg sizes in hatchery-reared salmon that are released with the intent of sustaining wild salmon populations. In wild populations, egg size is smaller in pops. with greater supplementation from hatchery fish than pops. with little supplementation. The implication is that the trait for smaller eggs is spreading into wild populations. Smaller eggs means smaller juvenile fish at hatching. Smaller fish tend to exhibit greater mortality which may cause population declines.
Volpe et al. 2000 Evidence of natural reproduction of aquaculture-escaped Atlantic salmon in a coastal British Columbia river. Conservation Biology 14:899-903.
Documents the capture of young non-native Atlantic salmon that were spawned in a river. Suggests that a feral population of Atlantic salmon arising from escaped aquaculture fish may be established in the Northeast Pacific.
While aquaculture may indeed be a viable alternative to traditional fisheries practices for many species, it is certainly not without its problems. Some of these problems I consider rather serious, and I certainly think about that when I am at the market. Unfortunatetly, that has meant that I don't eat much in the way of tasty seafood.
Hope this info. is helpful. It's good to see people thinking about conservation.