It's clear that it is the connotations of the rock, rather than the rock itself that caused issues - obviously ascribing social attitudes to inanimate objects only works if you are a headline writer for a tabloid newspaper.
I am inclined to agree with danny - it would have been easier and far more practical simply to re-name the rock, and maybe attack a plaque showing its previous provenance.
Education is a far better way to explain to people about previous attitudes that are no longer viewed as acceptable - and it's certainly far better than simply hiding something away.
History has its shameful times and actions, but that does not mean that we should be ashamed of it - history is what makes us who and what we are.