I don’t fault the shop for the CEL coming on now because an overheated engine can suffer problems at the time or problems at any point later on.
Once the temp gauge is on the H it’s often too late and continuing to drive the vehicle just exacerbated the problem even more.
Not being privy to the conversation between you and the service writer at the counter or knowing what was said between the service writer and the mechanic or the mechanic’s line of thinking I will say that it’s at least possible they could have done something that is at least ill-advised for want of a better term.
IF the service writer was made aware of the entire story about the overheating and IF this was written down or related verbally (bad move when it comes to oral arguments) then the first thing I would have done before even replacing a water pump would be to run a compression test and make sure there is no internal engine damage before spending one dime on the vehicle.
Even if the mechanic got a repair order that only stated “Replace water pump” he should be far sighted enough to ask some questions about the problem before digging into it and replacing anything.