I had something like that happen. I had to rewrite the whole story on the fly and kept hinting at the big, important mystery that they missed out because they killed the people necessary for the initial hook of the quest.
One of the things I like about the CofD games like Mage is it has a mechanical tracker for doing vile stuff. "Sure, you can curse him to vomit forever but that's going to call for a Wisdom check." Losing wisdom means you're worse at containing spell miscasts. Uncontained spell paradoxes will ruin your day. And hitting wisdom 0 means the character is unplayable.
I've stopped a lot of nonsense with "that'll be a wisdom check, if you're sure you want to do that"