As an EE, I've had a couple jobs where I worked on weapons. In fact, I've worked on the Conventional Trident Modification program referenced by TFA. It can be a bit of a struggle to deal with the fact that you're building a weapon. There's one rational that got tossed around quite a bit:
The weapons will be built by someone. Would you really want the weapon design to fall only to engineers that couldn't get other jobs? Given that I worked on the guidance parts, I could be glad that I was involved in making sure the weapon only went where it was intended to go.
Granted, that first part is a bit of a strawman, but it's based in the reality that not all engineers will ever stop working on weapons.
In the past, I've also worked on a torpedo project. That was a bit easier since torpedos are rarely used against anything other than a naval vessel, especially the MK48. Missiles are definitely more taxing on moral. Also, the fact that you're working on a weapon was always present for me and affected every single design decision. I wish I could say the same seemed true for the management. I'm not sure how many times I said things like "We're building a damn missile here, how about we double check that?"