2004 Chrysler Pacifica Check engine light stays on now after recent repair

It’s entirely possible that any current problem was created by overheating the engine.
You state the temp light came on and the gauge showed very hot. This means severe overheating has already occurred.

You state that you pulled over, saw no leaks, etc. and “immediately took it to the dealership”. Does this mean you had it towed or drove it? The latter is a bad move.

Since the water pump was apparently gone the reason you may not have seen any leaks is because all of the coolant was way back down the road and out of sight.

It’s also possible that any O2 sensor and catalytic converter codes could be due to the prior overheating along with a possible head gasket breach.
Stopping the car with a gauge pegging hot is closing the barn door after the horses done run off.

At this point I see that the dealer was presented a 7 year old, 140k miles vehicle that you bought used and had been severely overheated. When a shop is faced with something like that all bets are off as to what problems may exist.