You can't just heal damage with spells and potions in CoC/DG
Well you CAN, but expect it to be horrifying and sanity-draining.
This is one of the bigger problems with running difficult situations in CoC/DG, PCs are not designed to be heroic characters and are instead very frail.
In your specific case, I would not break their legs, but make them still take that same damage and walk with a limp (just assign a negative modifier to physical actions involving their legs such as climb, dodge, etc.)
As you say, if a person is not able to contribute to the adventure, it pretty much makes for a boring or frustrating game. It's best to avoid falling into those situations (no pun intended) by being a bit more lenient BEFORE the final confrontation, and then not holding back when they face the BBEG.