I'm not an expert in condensed-matter theory. I come more from the HEP/Nuclear physics side. I guess you mean this paper by Nambu
http://dx.doi.org/10.1103/PhysRev.117.648
I've to study it first.
What's clear from glancing over it is that indeed if you apply the formalism of self-consistent approximations known as the Cornwall-Jackiw-Tomboulis, 2PI, or (most justified in the sense of priority) the Baym \Phi functional in general you break gauge invariance. If the BCS theory can be represented as such an approximation (and the Hartree-Fock approximation is one) it's indeed likely that gauge invariance is violated. As I said, I have to study Nambu's paper first.
What I know a bit better is the effective model discussed in Weinberg's book, and that's simply the Higgsed scalar electrodynamics. The Higgs mechanism does not lead to a violation of gauge invariance, which is the trick also played in the electroweak sector of the standard model, which is (thanks to the charge structure of the quarks and leptons) gauge invariant. One should not call this spontaneous symmetry breaking, because Higgsing a local gauge symmetry does not lead to a degenerate ground state. The point is that the gauge invariance is local and you can transform from one vacuum to the other by a gauge transformation, and states that are connected by a gauge transformation are to be seen as the same state.
Of course, we usually break the gauge invariance by fixing a gauge, but again it is very important to see that the observable physical outcomes of this procedure (known as the Faddeev-Popov formalism when using the path-integral approach, which is most convenient here) are independent of the choice of gauge.
One particular gauge in Higgsed models is the "unitary gauge". There you choose a gauge such as to absorb the "would-be Goldstone modes" (i.e., those field degrees of freedom which would represent Goldstone bosons in the same model where the symmetry is global) completely into the gauge fields. Through this procedure you only have fields that represent the particle spectrum (and Faddeev-Popov ghosts which interact in the non-Abelian case compensating the unphysical fourth time-like component of the gauge bosons). The eaten-up would-be Goldstone modes provide the third 3D-longitudinal component to the massive vector field, which is absent for massless vector fields. If the original theory is superficially renormalizable, the unitary-gauge fixed Lagrangian unfortunately is not. That's why one chooses other gauges.
A very clever choice is due to 't Hooft (Nobel prize for this work!): You choose a somewhat modified Lorenz-gauge condition, known as R_{\xi} gauges, such as to get rid of cumbersome mixing terms between the Higgs field and the gauge bosons. Then the would-be Goldstone bosons stay as part of the field-degrees of freedom, but when you calculate Feynman diagrams for Green's functions in this now manifestly renormalizable gauge fixed realization of the model you realize that these would-be Goldstone modes cancel unphysical degrees of freedom from the gauge fields. In the non-Abelian case you also have to take into account the Faddeev-Popov ghosts, and then you end up with gauge-invariant S-matrix element, and these S-matrix elements are gauge invariant. At the same time the S-matrix is unitary, because you can take a limit, \xi \rightarrow \infty, leading to the unitary gauge. Since the S-matrix does not depend on the gauge-fixing parameter \xi you see that your model leads to a unitary S-matrix.
Now, the effective theory for superconductivity, described in Weinberg's book is nothing else than Higgsed QED, which is manifestly gauge invariant. This holds of course also true for the many-body formalism (Matsubara or real-time Keldysh or thermal field dynamics, whatever you prefer). So for sure there are gauge-invariant formulations for superconductivity, and I guess you can also make the BCS theory gauge invariant somehow. As I said, I've to read Nambu's paper first, to understand this in terms of the condensed-matter community.
You find Weinberg's approach to superconductivity also online:
S. Weinberg, Superconductivity for Particular Theorists, Prog. Theor. Phys. Supplement (1986) 86 43-53.
doi: 10.1143/PTPS.86.43
On the other hand, I don't see what's your argument what should be wrong with Greiter's paper.