There're two approaches here.
First is to notice that the specific presentation of the Pauli matrices is not predetermined. As long as those matrices satisfy the correct commutation and anti-commutation relations, ## [\sigma_i, \sigma_j] = 2i \epsilon_{ijk}\sigma_k ## and ## \{\sigma_i, \sigma_j \} = \delta_{ij} ##, they would do. For example, there's nothing wrong in choosing
$$
\sigma_x = \frac{1}{4}
\begin{pmatrix}
\sqrt{6} & 2 + i \sqrt{6} \\
2 - i \sqrt{6} & -\sqrt{6}
\end{pmatrix},
\sigma_y = \frac{1}{4}
\begin{pmatrix}
-\sqrt{2} & \sqrt{10 - i 4 \sqrt{6}} \\
\sqrt{10 + i 4 \sqrt{6}} & \sqrt{2}
\end{pmatrix},
\sigma_z = \frac{1}{2}
\begin{pmatrix}
\sqrt{2} & - i \sqrt{2} \\
i \sqrt{2} & - \sqrt{2}
\end{pmatrix}.
$$
The question is just what's the meaning of the components of the spinor. When we choose ## \sigma_z = diag(1, -1)## the components correspond to amplitudes to be at different sub-lattices, ##\psi_{1,2}##. But one can orient the quantization axis in any way one wants. What if I want the components to be symmetric and antisymmetric combinations of #\psi_{1,2}#. I can do that but the form of the ##\sigma## matrices will change. The representation above, for instance, corresponds to some specific choice of the quantization axis.
This has the direct relation to the rotational symmetry of graphene's Hamiltonian ## H = p_i \sigma_i##. After rotation around the ##z## axis, we have
$$
\widehat{R}(\theta) H = p_i \widetilde{\sigma}_i.
$$
So, we got Hamiltonian with slightly modified ##\sigma## matrices. if we ask ourselves, what do these new ##\widetilde{\sigma}## matrices correspond to, we'll see that they take this form if we rotate the pseudospin coordinate system around the ##z## axis. This makes sense: if we rotate the system, we need to rotate all objects, including spinors.
The second approach is to notice right away that
$$
\widehat{R}(\theta) H = e^{i \sigma_z \theta/2}H e^{-i \sigma_z \theta/2},
$$
which formally expresses the argument above.
And, of course, this is not a gauge transformation.