As pretty much everyone else on here has said, those prices you were quoted are ridiculous. You'd be getting hosed if you paid that much.
Radiator $578: Generally an easy job, the rad. itself you could probably pick up for $200ish or less.
Hoses $58: Um, no. Assuming only upper+lower radiator hoses are quoted here, those should be somewhere between $10 and 20 each and are a very easy job (4 clamps), esp. if the radiator is out already.
Coolant flush $100: Some benefit to having this done, as it cleans out the coolant passages in the motor. However, you seem to have determined that the cause of the overheating is due to the broken radiator, so this probably is unnecessary. Just put in all new coolant when you change the rad. Total cost: $5.
Thermostat $157: No. A thermostat is usually between $5-10, and the gasket is about $1-2. It's a very good idea to replace it when you're doing the radiator, since the cooling system is drained anyways and the part is cheap. This is also an easy job - usually a thermostat housing is like 2 bolts.
Ball joints $375: Not too sure on labor (I've never had to do them) but the parts are probably less than $100.
Brake fluid flush $75: Probably not necessary.
Alignment $70: Does the car seem to pull to one side? Vibrate at high speeds? If so, this should be done, but $70 is high for that. I just got an alignment done on my car and it cost me $35 with a $10 off coupon.
At least you're doing the right thing by asking on here. My parents recently took my brother's 94 Mustang in to the dealer for repairs without asking me about it first.
They ended up paying $420 for 6 spark plugs and a set of wires :|. That fvcking dealership had the audacity to charge them $8 apiece for regular spark plugs, PLUS 3 hours labor, and way too much for the wires (don't remember the exact amount.) I could have done the plugs and wires for probably @60 + my time spent on it (nowhere near 3 hours, I can tell you that much).
And people wonder why automotive service facilities are universally hated.