Shouldn't it be 'innocent until proven guilty' in this case? This certainly spreads some negative advertisement for Github. If the case is not clear, they should wait till it's clear.
That seems entirely guilty (if you want to make it into an issue of guilt)to me. github did have "mistakes and errors of judgment" serious enough that Tom resigned.
It cannot automatically be assumed that those considerations generalize to other contexts -- they must be considered in each context.