"No one will ever forget the terrible Hillsborough tragedy, nor those who died and their loved ones.
"But trashing a young man of whom everyone should be proud is not the way to honour their memory."
The editorial line of the paper remains defiant, accusing "local media" of whipping up controversy over the Rooney signing.
It also reports that the footballer, and his fiancee Coleen McLoughlin, have been "hurt and upset" by the criticism in his home city.
The revelation of the deal last week shocked fans of both Liverpool and his own club Everton, with many dismayed that the youngster was not better advised.
Internet message boards were inundated with messages from supporters condemning Rooney's deal.
The Sun made its original allegations - which were proven to have no factual basis - in April, 1989, under a headline declaring "The Truth."
Copies of the newspaper were burned on the streets and a boycott followed, which saw sales of the paper plummet across the region. They have never fully recovered.
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