You are correct, the headline makes it appear that he was refuting that it was genocide which is not what he said or did.
This is a charged issue between Armenia and Turkey. It's inconceivable the White House isn't aware of that. GWB may not be refuting that the forced exile and mass killings of as many as 1.5 million Armenians constitutes genocide, but he's making a conscious political decision not to call a spade a space.
The considered choice of the nearly benign word 'tragedy' which invokes a natural event, an expression of God's will rather than man's, like an earthquake instead of the much more accurate and honest 'genocide' which invokes a concerted act of man's will rather than God's is possibly expedient but certainly cowardly.
Given the choice of two words, tragedy or attack, to describe Sept. 11th would either of you use the former?