[pushkins]

It's hard to say exactly what your cost should or shouldn't be for the replacement of the single faucet as the "actual" work performed or time it took are not mentioned.

I do have to say though, that I think $600 is extremely high.

The "whole system" shouldn't need draining (no shut off valve at faucet location), especially as you mention the faulty faucet was upstairs, with the house's main water turned off the system would need only to be drained to below the faucet height itself. The actual act of replacing the faucet isn't all that difficult and depending on accessibility shouldn't take all that long.
You didn't mention the actual time the plumber spent on the job or the day that they came, if they need to make an out of hours call (nights or weekends) then naturally the per hour charges are increased.

As I mentioned above, I believe that at least on the surface from your given information $600 seems very high, a maximum three hour window for a simple faucet swap out (you supplied the faucet) would seem reasonable.
Even at $100/hour with three hours including travel (if charged) would make the bill $300.
If you have a record of the actual time the plumber spent on the job (plus some companies will charge a "service call") this will give you an hourly rate, this will give you a better idea (and arguing point) with the company.