Although it may be rare, there are other members on second generation Sienna's that have had their pumps fail prematurely. Labour rates are from Toyota dealerships and yes they can be that steep. Looks like they want to replace all seals since you have a possible coolant leak.
To get at the pump the Timing belt needs to be removed (the belt drives the water pump pulley). If the coolant has been leaking, it will have been leaking all over the belt. You don't want to do all that labour and keep the old belt that has been covered in coolant.
See my post for my pictures on the timing belt job I did this past summer.
you will see a picture of the water pump. which is in the middle of the configuration.
I would buy the Toyota oem parts from 1sttoyotaparts.com or another online Toyota parts seller which can save you around %50 compared to your stealership. Supply your own parts and save around $100 to $150 by just doing this (this is for the Timing belt and Water pump).
Before doing this, I would make sure the vehicle is losing coolant. Is the coolant level low, engine overheating, puddle forming on the driveway or garage floor?
If you do need the repair, then maybe you can have a friendly talk with the service manager and ask them if they can lower their labour charge out of goodwill. He may be a jerk, but at least you could try before proceeding with repairs. It maybe be that the water pump gasket could have failed (the gasket is metal with a rubber type gasket on the surface).
Good luck and keep us posted.
FYI doing this job yourself would be a huge effort (I did it, but for most they wouldn't have the patience and wouldn't want to risk it).