Removing baryonic material would mean all matter and dark matter are removed. Fundamentally a bad thing to lose all your protons, among assorted other atomic elements ;-)
In the movie, unprecedented solar activity accompanied by huge solar flares bombard the earth with multiple orders of magnitude more neutrinos than ever before. In the movie they are referred to as “mutated neutrinos” (snicker) because they are behaving like no neutrino has ever before. [ this is the Deus est Machina/ ‘magic occurs here’ of the movie ]. These “mutated neutrinos” act like microwaves to heat and liquify the earth’s core to the point where tectonic plates shift and portions of the earth crust liquefy — with predictable disaster porn results.
As you wrote, “normal” neutrinos are deomnstrably harmless, but these Mayan calendar neutrinos have mutated ... zombie neutrinos ;-)
Aside from that, the movie is ‘true’ enough to be enjoyable as science fiction drama.
Maybe reverse polarity neutrinos?
The stupid...it hurts!
If these neutrinos were powerful enough to melt the Earth's core, why didn't they vaporize everything and everybody on the Earth's surface on their way there?
And for that matter, just how do stone-age Mayans manage to predict a solar flare centuries in their future?