Will using it give the wrong impression?
Well, it will give the impression (if interpreted that way) of being a pop culture reference when it's not, but I assume that's not what you mean.
It's not as obviously problematic as if, say, the HG characters were simply rolling dice to see who survived, or devoting significant resources to invoking the favor of their gods, or some such antirationalist meme; the movie is at least nodding in the direction of game theoretical concerns, if not necessarily showing much insight into them. So it could be worse.
Is there any rationalist equivalent of "good luck"? I've tried a few variants, such as "work well", "knock them dead", "we're with you" and certain situation-specific phrasings, but haven't found anything that worked generally - though a hearty "may all the gods of Olympus be with you!" can serve. Not a vitally important point, but it would be nice to have something similarly supportive and yet accurate to say.