Not really. He made these comments when the genocide had become common knowledge, and the facts had been accepted by anyone conversant with the situation in the region. His continuing denial was based on the flimsiest scraps of evidence, and people were generally dumbfounded by his obtuseness in this matter. When you deny a genocide, it’s not merely a difference of opinion, it has a moral dimension, as when people deny the holocaust.

Look at the totality of his comments:

They wrote that the refugee stories of Khmer Rouge atrocities should be treated with great "care and caution" because "refugees are frightened and defenseless, at the mercy of alien forces. They naturally tend to report what they believe their interlocuters wish to hear."

It's quite ironic that it was Chomsky himself who was dismissing evidence that didn't fit with his own world view.