Well, if you outlawed every form of argument a simpleton can misconstrue, you might as well cut your own tongue out.
Literature is great way of raising questions. It's a lousy way of *answering* them. You should never walk away from a book convinced of anything, whether it is science fiction, historical drama, or a Harlequin romance. That's because an author controls the domain of discourse in fiction. He creates the fiction world and as much of its history, natural science, and society as suits his purpose. He can produce a socialist utopia or a Galt's Gulch, whichever serves his story -- or his biases.
As for the science fiction fan's supposed knowledge of nature, I'd be suspicious of it. While it's true that sci-fi fans often have familiarity with physical science and technology that exceeds the general public, that's hardly a ringing endorsement. In my writing group, I recently critiqued a manuscript in which Shiite terrorists, working under a Wahhabist imam, build a lithium deuteride super-warhead and launch it on an ICBM into equatorial orbit to cause world-wide destruction of electronic equipment via EMP. Now virtually *every* aspect of this scenario is demonstrably *wrong*. When I pointed this out, the author's reaction was "It doesn't matter." Now there's something to be said for this. All he really needs is the set-up for his post-apocalyptic adventure, and it could just as well be magic and pixie dust as EMP and lithium deuteride. But I feel that as far as you explain anything, that explanation ought to hold water.
The thing about scientific literacy is that it isn't knowledge of a bunch of random, disconnected facts (e.g. lithium deuteride is used in thermonuclear warheads) as it is a capacity to figure things out, like whether it is remotely feasible to take out the entire world with EMP from a single warhead. Basic fact-finding and simple computation.