the baddies planned to take survivors prisoner
This, right here? Gold. (Just don't use it every time or your players will begin to assume you'll never kill them.)
Yes absolutely, and I should have mentioned it myself.
You have to make sure being taken prisoner makes the right kind of sense for the situation - basically any time that being taken prisoner doesn't
feel like a "safety net" so much as an "out of the frying pan, into the fire" sort of moment.
In my above example, the captors present the PCs with a simple decision: slave labor building the temple (that the PCs came to destroy in the name of one's god), or be fed live to the extremely large lizards kept as beasts of burden.