1. I would probably just keep the waterpump. You are going to need it sooner or later anyway. If not, just sell it.
2. By your own experience, you have just proven a key point, which is that estimates are sometimes best guesses, based upon the knowledge and experience of the person doing the estimating (which is a big variable). Very often, it is impossible to know the root cause of a problem without actually getting into it and taking some things apart. Once you do that, sometimes you get lucky and find an easy problem right away as you did, or sometimes it takes considerable troubleshooting to get to the root cause of a problem. Once in a while, things can turn to poope even for the best technicians with the best intentions.
3. In this case, since it seems obvious that the guy never did even the most basic troubleshooting, I think you would be justified in bringing this concern to the attention of the Service Advisor. Most businesses really do want to keep you coming back, and will comply with a reasonable request such as this, especially if you are an established customer.
Good luck, and please let us know the outcome.
2004 C240 Wagon 203.261 Baby Benz
2008 ML320 CDI Highway Cruiser
2006 Toyota Prius, Saving the Planet @ 48 mpg
2000 F-150, Destroying the Planet @ 20 mpg
And remember folks, Only You Can Prevent Hilliary.