Not sure why you're using field theory to compute this process, unless you're at energies much higher than the QCD scale, in which case you'd be using perturbative QCD. In this case, the issue is irrelevant because the degrees of freedom there are quarks and gluons.
Two nucleons
can interact via a contact interaction at low energies ala
this paper. But don't take such a contact interaction literally; Feynman diagrams are equivalent to propagators which actually describe amplitudes in terms of wave mechanics. It is certainly possible for two identical fermions to have overlapping wave functions.
I think another source of your confusion is stemming from thinking about bound systems, whose spectra are discrete. A bound state can be described by \left\lfloor n \, (L\, S) J \, M_J ... \right\rangle, where the "..." denotes the possibility of internal degrees of freedom. In this case, you definitely can't put two fermions in a state where all the quantum numbers are the same. But in scattering states, a continuum of states is possible: \left\lfloor n \, (L\, S) J \, M_J ... \right\rangle \rightarrow \left\lfloor E \, (L\, S) J \, M_J .. \right\rangle. Asymptotically, the overlap between two protons in a scattering experiment is zero, and their indistinguishability can be neglected.