They don't actually flush them live - they'd be breaking far too many of their policies with that. Of course, the store manager might not care, but still. I don't know Georgia's policy on it, but in Maryland, dead fish must be bagged and put in freezers to be shipped out to whatever company handles disposal - same with all deceased animals in care of a pet store.
They probably take them back, change the water, wait for you to leave, then put them back on the shelf - they'd try to give the illusion of some care, if nothing else. If it's a common enough disease to take care of (Ich, etc), and they have the medicine available, they may treat the betta in the cup.
Avalon - Male Butterfly Double-Tail Halfmoon, Pink/Cellophane
Camelot - Male Marble Double-Tail Halfmoon, Black/White
Merlin - Male Delta, Steel Blue/Green