Is this a late 2012 model or late 2013 model with the PCIe SSD?
I'm guessing it must be the late 2012 model, as the late 2013 should still be covered by the Apple warranty and you wouldn't be worried about the cost.
Yes the Apple SSDs are very expensive as they use their own unique physical interface and form factor, instead of going with a standard format such as mSATA. There are other choices for the late 2012 rMBP, if you have the right tools or a repairer who can carry out the job. OWC make replacement SSDs for the late 2012 rMBP and just recently Transcend has started offering replacement drives.
Of course if there is water damage, perhaps other things are damaged too. If the mac shop agreed to "fix everything" for that price, it might be worth considering.