I don't think the torpedoes were armed, but I also don't think they were untraceable. Once the Enterprise launched the torpedoes, the Klingons would've spotted them and shot them down then went after the Enterprise. Which Marcus would claim had gone rogue.
Plus, I think Marcus knew exactly where Khan went. Why else would he have allowed Enterprise crewmembers around the wreckage?
Once Pike was dead, he was counting on Kirk going off half-cocked after Khan with revenge on his mind.