Well, one thing that happens that appears to be a leak, unless they determined this via pressure/cycle test, is that the box will back up with water if the A/C condensation drip tube is kinked or clogged.
It is not hard as it is just like a small radiator. The thing that is hard about it and costs money is recycling the R-134a. You would just let it go into the atomosphere by pushing schrader valve on tube in engine compartment where it is filled. But, you should be carefull when cracking open every connection as pressure can be on either side of the system. There are a few items to transfer off the evaporator that you have to be carful with as they are somewhat fragile. You just remove the box on the right under the dash above the blower motor and you will see the evaporator. You will have to get it filled and oiled when you are finished. It would not be a bad idea to get some R-134a refrigerant from your parts store, make sure it is type with oil in it or it is not worht doing, and add just a little as anything over a pound or so can be too much in a lot of systems. That should give you some extra protection on the way to the repair shop to get it evacuated and filled. A thousand is aboout right as I used an estimator program and got $750.00-$1005.00. So, by the time you deal with all the stuff and you will have to do a bad thing by dumping refrigerant into atomosphere, it is a good price. High end, but in range. You might try to talk him down a little or at least make sure he uses good parts. You should get at least a 1 year warranty. Maybe more, but if it is less than 1 year, I would take it elsewhere. Four Seasons is a good and common A/C aftermarket replacement company.