The difference between color-superconductivity and ordinary electron-superconductivity is that the dynamics is treated relativistically (because it's often high-density that is discussed), so in expressions such as $\langle q q\rangle$, the $q$ is still relativistically quantized. But the thermal state certainly breaks manifest covariance. (Aside: maybe I should also say, another difference is that in color-superductivity there's an obvious channel for pairing, i.e. color-Coulomb interaction, which is a plain QCD effect; while in normal electron superconductivity, the pairing mechanism is much subtler, i.e. phonon exchange. In this sense, color-superconductivity theory is much closer to QCD than electron-superconductivity to QED.)