Vickers (a woman) brings a magical auto-surgery machine on a trillion dollar mission that's only calibrated for men?  Doesn't strike me as the type to forget a little detail like that.

Like anyone is going to listen to the scientist who says don't bring weapons.

Like any scientist would take off their helmet in a strange new atmosphere with unknown biology.

Or that they'd just jump out and start exploring without sending the orbital equivalents of the survey robots, and sending a less intelligent robot first.

Or that a guy with worms crawling out his eyes on a strange planet wouldn't be headed straight for sick bay.  And might tell the woman he loves and just had sex with cause she's been exposed too.

I'll skip all the sound-in-space ("In space, no one can hear you scream over the sound of ion drives") and relative structural strength arguments (a huge spacecraft is so delicate that it gets taken out by a tiny ship, but then is structurally sound enough that it can roll around on a planet?  And the Engineer (thanks!) survives the crash?

Why would the Engineers create Aliens to destroy the earth if they were displeased?  Obviously they could simply use the same DNA tech to create a disease which would simply wipe out the human population with the release of a vial, say, not unlike the one used to create life on earth in the first place, and at much less expense than the 8-10 ships we saw in that valley.  And with less risk to themselves - witness, the Aliens killed the Engineers on that planet.  Surely the Engineers known about Level 4 (or 5) biohazard safety precautions, and a virus is easier to handle than an intelligent, malevolent, acid-blooded mutating creature.  We must have really pissed them off 2000 years ago when they started this program.