A lot of people seem to get hung up on the idea, (that they dislike) of the alien get sexual pleasure out of this rape. I've always seen it as a violation, horrifying and a sexual assault from Lambert's perspective, but from the alien just as sort of rythmic examination that was a too violent for Lambert to survive.
But yeah, the imagery is all there throughout the film, and the tail between the legs, and the jolt reaction from Lambert, all suggest that basically she was sexually violated to death. I'd call that rape, but others seem to require an alien penis and alien sexual pleasure to be part of the 'rape' scenario.