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You can't properly setup the differential gears without removing the pinion. I have a real hard time believing they replaced the carrier, and got it properly shimmed without touching the pinion shims.
Key word! ^
With that said, some do believe you can replace a carrier and just set the lash, because you are not affecting the mesh if you don't move the pinion in or out.
What I don't accept is they knew it was leaking, they should of not agreed to do the job without planning on fixing the obvious leak as well!
At that point it's just a few more bux in the big picture of it all!
Now the OP has to pay the labor to do half the work twice costing him 1.5 times more than it would have to do it right the first time!
I would have refused the job if the customer insisted or done it (the seal) on me!