Ridley's actual view of what was going on with Lambert when he talked about it in the Alien Quadrilogy commentary, where he seems to suggest that he accepted the implications of the sexual ambiguity of the scene and if he's changed his view since then, well, that's up to him.
Ridley Scott: I mean we didn't know how she died but er, the implication that there was a kind of sexuality to this androgenous male/female who could give birth itself, it could also impregnate, so it's like a , there are insects like that, we based that on a , you know a little bit of good old mother nature and erm, was that some dreadful ending, was that some terrible you know invasion of her body, a rape and therefore would there be a version of the Cartwright character. There'll certainly whatever happens, there'd be more humanoid aliens now on board this craft and that's what she's now got to destroy.