Simple: You hit escape when you're solo in a dungeon, and the game pauses.
I shouldn't really even have to explain why such a feature is necessary, should I? A full T3 clockwork run takes about an hour, and any amount of things could happen within that timespan without conveniently overlapping with a point in time where you've not being pelted by TVs and office supplies: Someone could ring the door, your cat could be trying to make kittens with your face, the phone could go off, your spouse could be bickering for the seventeenth time about how she's feels like you don't love her as much as videgames and it's really not helping your case if you have to tell her "Hold on, sweetheart, I love you very much but you need to give me about twenty minutes to finish off the entirety of heart of ice because if I look away from the screen for just five seconds the endlessly respawning lost souls will kill me." Maybe your dog is chewing on the power cables and it'd totally ruin your game if the dog were to electrocute itself on exposed wires, causing the fuses to blow.
So yeah, pause button. It'd be swell. Don't say it can't be done, Warframe does it.
DO THIS. Many games allow it, why not Spiral Knights? It's annoying when I can't even run to the bathroom safely unless I'm behind a force field or far, far away from any enemies.