We don't know what they took out.
But they could have toned down a sexual undercurrent.
Anyway, I don't know how you do a PG-13 p*ssy burster. Sorry in advance. That sounds horrible.
Well... I'm pretty sure said lil "Vaginal Excavator" (Makes the space squid sound like a bull fighter... Or something.) is actually just a glorified and horrifying c-section.
There's a scene in "Time After Time" right at the beginning of the film. We see from Jack The Ripper's POV as he stalks a woman and kills her in an alley. We see a little blood, very little... But we never see the knife penetrate her, and we only see the look on her face, and the sound of fabric tear. It's an incredibly effective moment.
...See, making the scenes in Prometheus unnerving is going to come down to the editing, acting, and sound. Not the gore. I trust Noomi to know how to act, because she does. I know Ridley can direct a damn good movie when he's got his A-game on.
So how would I personally shoot this scene to be intense, yet PG-13 friendly?
Shoot pretty much the same way Scott has. Using lots of close up shots on Noomi, shooting across her body, putting things in the extreme foreground of the frame in front of her so we can't quite see what the thing is. (It's very reflective of her own perspective. She's strapped in, with limited view of these things happening right in front of her. TO HER.)
Have her strapped in, the arm comes down and starts cutting her open to extract this thing. We watch her reaction as she looks away, biting down on her lip, trying to stifle cries of pain, afraid to look at whatever might be inside of her.
We don't have to see the gaping hole in her side where this thing is extracted to get the horror of the scene. The vulnerability is going to be in the actresses face. That's where the focus should be if you want this to be adult and real. Not on a bunch of effects. You use those to season the scene, of course. (showing a shot of her stomach with something moving under the skin. Something bulging up.) but you don't have to have gobs and gobs of blood and blood everywhere to make it work.
The reason the burster scene is so damned good isn't the gore. Though it's all done very well. What really sells it are those actors who are giving such a fantastic performance, and the great use of editing.