I know one scenario with a negative boon at the end on the chronicle indicating you get captured and tortured. To me, that implies that if they want to say you get captured instead of killed it will be made explicit.
I disagree. There are plenty of situations where the NPCs don't have any motivation to kill the PCs.
This one is pretty obvious. When I ran it the first time, I had 3 experienced players breaking in new characters, along with a pregen. I actually had all 3 PCs down to negatives, with the pregen cleric running away from a Cause Fear spell, and I decided the slaver would want to keep them alive, and also be arrogant enough to think the cleric wouldn't come back. When the pregen cleric came back two rounds later, she channeled to wake up the PCs, and the fight was back on.
In conversations about another adventure where the final fight is against muggers (most of you know what scenario I'm talking about), majority opinion here on the forums has been that the muggers will just take the PCs' stuff and not care if they live or die, so they could be left bleeding in the street to stabilize on their own.
Unfortunately, this particular scenario is really rough for a group of new level 1 PCs. We've talked for years about how some subtier 1-2 adventures are fine for a bunch of level 1s, while others require at least a couple of level 2s to have a good chance to win, and it would be nice if they were labeled as such.
But it also sounds like your GM messed up the tactics - that cleric is supposed to start out just healing the undead minion with channels, not blasting the party right away. The tactics seem to be intentionally written that way to keep the adventure from being too lethal.