I think that for a "real" proton and electron, the full quantum mechanical state would also encode quantum numbers like electric charge, lepton number, baryon number, etc which would differ for both particles and (most of which) we believe to be conserved.
Also (but I'm not really sure about this argument): note that a proton and an electron have very different masses, so they satisfy different Schroedinger equations (which contains m). Therefore, even if you put them in the same state, when you measure a property (like the energy) they cannot in general collapse to the same state because they don't share (all) eigenfunctions.
(Afterthought:) on the other hand, if two wavefunctions are exactly the same, any information we can extract from the wave function will also be the same so it's really no use to try and distinguish between two such particles. I.e. we have agreed that "by definition" an electron is the particle which, when I measure property such and so, I will get this and that value. So if a proton would give the same values, it wouldn't really be a proton, but an electron anyway.