It's not impossible that there's some other factor in play there that is yet undiscovered, and Neutrinos would make sense as an object that would demonstrate the presence of the factor.
Neutrinos, have very low mass, and pass through objects with ease, and are electrically neutral. They're pretty different from the particles we know very well, like electrons and protons.
Conceivably, there could be some other factor that falls outside of our range of senses, that functions as a constant on a macroscopic scale in our atmosphere and under our gravity, but has a different value outside of it. We have very little data, if any real data, outside of the realm of our solar system, and precious little data outside of our planet. We've made alot of assumptions that what holds true here, holds true everywhere. There's no reason the actual equation couldn't be E/X = MC^2 where X is some factor we haven't yet recognized.
Don't get me wrong, Einstein was an unparalleled Genius I wouldn't compare to even if he were sleeping, I'm just saying he made his discoveries based on what we know, and there's no reason there couldn't be a factor that has remained constant in our experiments thus far, but is actually capable of varying. Something outside the realm of our senses, and thus far undiscovered because we haven't had direct inference of it's effect yet.