Q: Timing belt and water pump replacement

Hello. I am sorry to hear of this. The seriousness and inconvenience of the circumstance you are writing in about is an excellent example of why dealing direct with a professional and cutting out the bureaucracy of what are becoming ever larger "repair centers" is good for real people. If you had an agreement with the Dealership, oral or written (it doesn’t matter insofar as consumer law in the U.S.), to replace the water pump IN CONJUNCTION WITH the replacement of the timing belt and they did not perform as promised, legally they are on the hook for remedying their failure.

In this case, the remedy is assuming the EXTRA cost of removing the belt (i.e., regaining access) and installing the pump. You were smart and proactive in requesting that the pump be replaced. It should be replaced and that’s WHY aftermarket timing kits include the pump! And, your supposition that their "after the fact" MTBF (mean time before failure) "statistics" are too good to be true is correct.

If it is true that water pumps on your specific year, make and model, have a "low" rate of failure, all they need do is show you the data but they do not have such data. The bottom line is you certainly should insist that they install the pump and also remind them that a new OEM Toyota thermostat should be installed as well. As far as the timing belt is concerned, I hope they installed new pulley bearings (the aftermarket kits include them as well for a very good reason: the grease in those bearings oxidizes due to the heat and then the pulleys eventually get noisy. Please let us know if you have further needs or concerns regarding this or any other repair on your vehicle.