Pop quiz: You tell someone that your pet gerbil (or whatever) died (or whatever). He says, “I’m sorry.” What do you say next?
If you think you should say, “It’s not your fault,” then it’s really no wonder that your hamster died. You’re evidently not very bright. Because it’s extremely unlikely that the other person was admitting to killing your pet when he said, “I’m sorry.” What he was doing, rather, is expressing sympathy (or the like). “I’m sorry” in this context or one similar is shorthand for “I’m sorry that your mole/vole/stoat passed away” or “I’m sorry to hear that (thing you just told me).”
So what you should say, if anything, is “That’s okay. It was just a ball of fur with a tail and teeth.” You should not say anything that suggests that you think the other person was confessing to rodenticide, because that makes you look both foolish and oddly suspicious and will lead only to awkwardness on top of a dead-pet situation.