is $650 to much to pay to replace a run capacitor and a contactor and put 6 lbs of Freon on in a central air conditioner unit ?

Six pounds is more than half the charge (probably). We are required to locate and repair leaks that size.
Contact the installer to fix it because that is not supposed to happen. Something went wrong on the install.
You will need Six pounds in another two years if you don't.

For a 2 year old unit I would scream like crazy to the manufacturer. 6 lbs of freon leaking is outrageous. The run capacitor and the contactor should not have failed in 2 years. A good quality contactor will last for 20 years, capacitors are also usually good for many years and a freon leak is just plain wrong. Contact the manufacturer and scream!

What kind of Freon was it? 22 410a ect please explain as there is an obvious cost difference to that. Look on the nameplate.

You may not have overpaid for what they claim to have done, but you WERE ripped off. A reputable contractor would have contacted the manufacturer regarding the warranty before doing ANY of what you describe on a 2 year old unit.