You did the correct thing by returning them.

I highly doubt they had the "protozoan infection"...everytime I QT a new fish it doesn't eat, but that is because of stress from the move from one tank to another.
so those angel fish are not "doomed" they'll have a better suited first home.

the pleco thing-this is a catch 22, they do outgrow tanks, but at the same time, they grow slower than normal fish. so i think you could keep him for a year or two and then look to trade it off.

substrate for cory's are highly debated things.
the flourite substrate isn't that sharp. many people keep cory's on that type of substrate. I currently have 8 cory's on pea sized gravel and everything is fine.
people claim now that the barbels get damaged because of water quality, not substrate.
my cory's are happy on their gravel, and your's can be too. they'll just be more happy if you had 1 species and 6 of them (as they are a schooling fish)