thehangedman,
Yes, there would be a non-uniform distribution of charge because of this. Effectively gravity creates an electric potential difference in a conductor on the order of:

Assuming there is only one type of charge carrier with mass m and charge q.
And yes, the effect would be very very small. You also would not be able to measure it with a voltmeter since the voltmeter would feel the same effect (that doesn't mean you can't detect its effect other ways though).
I didn't read your references, but if they did use a liquid conductor to see these effects, it is probably for exactly that reason ... the charge carriers are very heavy, making the effect bigger and easier to detect.
Getting back to your main question, no, this would not ruin a superconductor.
Instead of a gravitational field, let's use an external constant electric field. Does this ruin superconductivity? No. Does it split the 'levels'? No.
Charge will just build up on the surface (like in an ordinary conductor), to "expell" the
electric field from the conductor. The superconductivity will continue as normal.
In both examples, the external force on the electrons was the same for
all electrons. So how could this possibly "split the levels"? It will not.
Imagine an external magnetic field. Since the electrons in the Cooper pair have different spin, they will feel a different force. But again, a superconductor will work to expell this field, and the superconductivity will remain in the bulk (until you exceed the ability of the superconductor to expell the field).
Hopefully that answered your question.