The large corporate pet stores vary quite wildly even within the chain. Much of it depends upon the people who work there. There is no criteria to find out who will work there so there are people there who work everyday to ensure the health of their animals and then there are people who don't know what newts are, think oscars do well in 10g aquaria and that hamsters are baby guinea pigs.
But even the best employees can't change huge corporate policy and sometimes the higher ups do odd things to try and earn more money. Our local Petco invests large amounts of money in marine fish that continually die through improper setup and care because people like to look at their pretty colors. This is despite the efforts of a very qualified aquatics person who just doesn't have the resources available.
I think Heather has quite a few very good point on the way our society treats animals and living creatures in general.
This doens't mean I don't think you should have sent the letter, you definitely should have! We have to stand up and point these things out and make the big wigs change their tunes. Signing your name to it is definitely a must as an anonymous letter is just so much trash.
As far as toxins go I would consider that only a problem if there were possible attack/feeding reactions with the tankmates. These animals don't continously produce toxins as that would be metabolically taxing and unnecessary.
Other good issues to include would be stress levels due to differing activity levels, crowding in the tank, lack of hiding spaces for one species and the bioload produced by a larger amount of animals in an enclosure.
Writing letters to PETA and telling them about Petco definitely gets their attention, but it doesn't seem to work with PetSmart all that well to my knowledge