My opinion, others may vary, is that it's not obvious in the film that the alien is blocking the entrance to the Narcissus. It just looks like she bumps into the alien somewhere and suddenly changes her mind about the self-destruct. It's a bit more telegraphed in the cut shot, because of the contrast between the safe-looking white area behind the alien and the dark technical corridor in front of it, and because the twin set of doors looks like an airlock.