Who locks their rodents in a freezer to kill them?! I would consider that suffering as well. The rodents we have were killed either by gassing or spinal separation.
We've had the occasional rat that 'just wouldn't give up', and it's heartbreaking to watch. Especially when the snake just didn't get the best grip on the rodent and it kills it in a weird and long lasting way. We even had a rodent...well..it's guts shot out. Alive. I definitely cried that night, it was awful. Usually it's 'quick', but often times the times when we think the rodent is dead it's still alive, just knocked out of has given up. Not fun to see what you thought was dead have one last two or three kicks much later on. I can understand feeling bad for the rodent. Honestly, the fact that Maru won't take f/t reliably drives me nuts, and it's kind of preventing me from wanting ball pythons in the future, due to their notorious nature for not accepting f/t prey.