Nope - the cancer was never from Dr. Manhattan; it was all set up by Adrian Veidt, quite intentionally, as a plot to get rid of Dr. Manhattan as too big of a threat to Adrian's plans. And, yes, it was actually in the comic, although it's easy to miss.
The Watchmen Wiki has this in the entry on Mars:
Mars is the fourth planet from the Sun in our Solar System. When Dr. Manhattan realizes, in late 1985, that he may have been inadvertently responsible for the cancer deaths of several friends, he leaves for the solitude of Mars. It is later revealed that he was framed for the deaths.
Then, from Dr. Manhattan's page:
During the execution of Adrian Veidt's plot to save the world, Manhattan is accused of giving cancer to those exposed to him over long periods of time. It emerges that this is untrue, for it is rather a careful fabrication of Veidt's, but this revelation is not quick enough to prevent Manhattan from exiling himself to Mars, where he spends much of the action of Watchmen.
and later, on the same page
He leaves Earth for Mars when he is accused of causing cancer in his close associates over the years. However, this was a frame arranged by Veidt to induce Osterman to leave, to remove his interference in his scheme to save the world
Then from Veidt's page:
To prevent Doctor Manhattan from interfering, he hired old associates of the superhero and secretly exposed them to radiation to induce terminal cancer in them, then engineered a rumor that Manhattan was responsible, causing Manhattan to exile himself to Mars.
And.. here's Veidt busily doing the whole 'Now that it's too late, let me tell you my evil plan' thing...
