Is the LHC going to Destroy the world?

And what makes you think a magnetic monopole would absorb protons in the first place? A magnetic monopole is, for the moment, a theoretical extrapolation. The properties of such a thing are merest speculation at this time. In which case what makes you think it wold do what you suggest? It's just a likely to just pop out of existence, or join another, opposite monopole and become a dipole.