Granted, in hindsight his doubt seems a little silly. But at the time, it made a lot of sense. Marvel had a lot of success in the 1960s but by the early 70s they failed to follow up with their greatest hits, and sales in the industry were down. Science fiction comics hadn't sold very well in the past, so it seemed reasonable for Marvel to reject a comic book adaptation from George Lucas. Luckily for Marvel, enough people disagreed with Lee. Their comic book adaptation was a top seller when the films were released.
And now Disney owns them both.
The comics didn't do well after the films were over (turns out nobody was interested in hearing more about Ewoks). And while the comics made in the leadup to the prequel series were nifty, Dark Horse Comics were making them, not Marvel. It wasn't until Lucasfilm was acquired by Disney that Marvel could bring the characters to life again. Seems kind of like they were destined to be together after all?