Mass-energy equivalence does not mean you have to measure mass and energy in the same units. For example, kilograms are not the same units as Joules.
In particle physics, eV, keV, MeV, GeV, TeV, etc. units are convenient ones, and if you implicitly assume that ##c = 1##, you can put a ##/ c^2## on any of the units without changing any numerical values. That's more or less what particle physicists do, but you have to be clear about what they are doing. They are not saying that mass units and energy units must be the same because of mass-energy equivalence. They are implicitly assuming that ##c = 1## in order to be able to not have to care about whether the units they are using are "mass" units or "energy" units. But that only works if you assume ##c = 1##. If you don't assume ##c = 1##, then you cannot say that, for example, MeV and MeV / c^2 are the same units, because if you don't assume ##c = 1##, they're not.
In your actual equation, you used MeV / c^2 everywhere, which is fine and doesn't require you to say whether you are assuming ##c = 1## or not. But it also has nothing to do with mass-energy equivalence.