The following is applicable to the Invincible Persons FAQ by oneirotekt, http://www.gamefaqs.com/xbox/561456-deus-ex-invisible-war/faqs/28072 I'm only posting here because there isn't an email in the FAQ itself.
In the Notes section, there's this entry: - Mag Rail Scientist: sparing him and picking up the weapon means you will fail the Order mission to assassinate him and complete the WTO mission. Once he's stepped into the sealed chamber to unlock the weapon you will be unable to harm him. Likewise, eliminating him before he steps into the chamber means you will be unable to pick up the mag rail.
This is slightly incorrect lol. You CAN both kill him and get the gun. You need a concussion prox mine and some speed - I think I did this fairly easily without the Speed Enhancment mod, but that would give you more elbow room here. Place the prox mine on alt-fire, and before it goes off run down and get the gun. Do this fast, as once he's dead it locks down. You'll complete the WTO objective instead of the Order objective, and if I remember right the guard right behind you will suddenly go aggro once he's dead, but the point is you can have your cake and eat it too lol.