Changing the makeup of the molecule IS what makes it safer. It doesn't magically make the nitrates disappear, it detoxifies them by making them unavailable.
Dechlorinators, like sodium thiosulfate (which I'm assuming Prime is essentially) do affect the toxicity of heavy metals! They can bind to the metals and alter them so they are in a form which is unavailable to organisms, therefore decreasing toxicity.
Oh, S.R., Kim, J.K., Lee, M.J., and K. Choi[SIZE=-1]. 2007. [/SIZE]
Dechlorination with sodium thiosulfate affects the toxicity of wastewater contaminated with copper, cadmium, nickel, or zinc. Environmental Toxicology 23(2):211-217.
Trihalomethanes can also form from chlorine use... which are irritants and carcinogens.
We use chlorine in water treatment to kill microorganisms, why would you want it in your tank? We want beneficial bacteria growth and know chlorine has a detrimental impact on fish... if your water source has chlorine, why wouldn't you dechlorinate it (Prime, dissipation, etc.)?
Dissipation isn't instant, and it'll definitely be pumping through your filters for a couple hours before the chlorine isn't gone. Doesn't mean you won't be able to keep fish, but I'm not going to risk chlorine exposure for any reason. If I know something I can't ignore it or risk my fish health!
Heck, water treatment plants dechlorinate the treated water before it goes back where it came from - obviously that is a hint!