In line with the part of the navigator's spiel about not holding everything to human terms, yes, if to the alien it was sexual intercourse, and the man did not consent, it is, by definition, rape. It doesn't matter if the man thinks of it that way, or if he even cares - the alien is by its own terms a rapist and that's what makes this creepy to me.
wakela - yeah, it's tough, but tough mainly in that we can't honestly predict what alien sexuality would be like. In the specific context of this story, there's one obvious possibility, though - if human speech is analogous to sex to these creatures, then a human coming to the planet and talking at an alien and not stopping if asked. If the creature isn't interested then that would be non-consensual sex and potentially very shocking to the aliens.
I hope that helps illustrate what I mean by the broader terms thing. If to at least one participant it is sex, and consent is not involved, then it's rape. Doesn't mean it has to be inherently harmful or unpleasant to either of them, especially if the standards held are widely different. Just means it's rape.
Edit: Also, most people instinctively feel violated at the idea of an anonymous sleazeball masturbating to them. I'm feeling that the videotaping and the story are different situations, possibly to do with the relative presence of the victim or something but I'm having difficulty explaining exactly why.