How did he not die from Salmonella after eating so many raw fish out at sea? I've re-read the novel and couldn't find evidence linking to him cooking the food (which isn't even that possible out at sea).
There's a whole cuisine that uses raw fish as a core ingredient (and the only ingredient in case of Sashimi). As long as he avoided eating the guts of the fish, and with a little luck, there's no reason why he shouldn't be able to survive on raw fish.
Given that he survived for months at sea, in real life it is likely that he would become infected by some parasites living in the flesh of the fish. The symptoms of those may be hard to distinguish from the symptoms of exhaustion, depending on what exactly gets him - and being parasites, they are not normally quickly fatal.
Another thing to consider is that we hear Pi's story second-hand, as he's telling it to the author. It may be that he simply left out the part of the story involving doctors surgically removing worms from his gut.
Just addressing Salmonella, it's not usually life threatening. Typically just causes moderate illness (but quite unpleasant) from which most folks recover. If you're in a risk group (compromised immune system for example), it can be life threatening.
The organism itself lives in the intestinal tracts of animals and not the fleshy, muscular tissues. You could fillet (or just chew) the fleshy parts out without ever cutting into the intestinal tract.
Similarly for many other types of organisms, they typically live in the intestinal tracts of animals. Of course, there are other nasties (some types of parasites) that inhabit the muscle tissues and the above approach doesn't help avoid them if you must eat raw fish. Pi was maybe just a bit lucky also.