Wait... Are you keeping 3 rats and 3 hoppers in a 2.5 gallon all together???
OP, did you put the rat in the freezer immediately after you euthanized it? Or was it in an area where it was constantly thawing a bit each time you opened the freezer? The rats shouldn't stink when you thaw them. I've only had it happen a few times when I bought them from an outside source.