If you believe that doing something is wrong, the idea that someone more unscrupulous will do it if you do not must not be used as an excuse for doing that thing yourself. Giving in to this notion will prove yourself to be the one who is unscrupulous.
By involving yourself, you gain the opportunity to do the right thing (for the given the circumstances). If quitting accomplishes the same thing as sabotage or internal lobbying, then by all means.
1. If you're on an active battlefield, both sides have already agreed that killing people is morally justified.
2. If the enemy is shooting at you, he is not interested in the ethics of killing someone on a battlefield.
3. If ethics helped wars end, there would be a US Army 27th Ethics Brigade to parachute in, but there's not and probably never will be.
If on a battlefield, given a choice between holding scrupulous ideals and living, most people would choose living.
If someone wasn't willing to kill someone else on your country's behalf, most likely you wouldn't have the freedom to ask that question.
Edited to add:
The metaphysical question you posted might be better phrased to ask:
What's the point of life if someone else is willing to extinguish it?
Well, given how unimaginative a leap the national socialists took from the national fumigation program to the gas chambers, I doubt there was much more to it than "take bug poison room tech, use it on humans".
There's no such thing as an "engineer" in the real world, and there's almost always somebody more unscrupulous, devout, or patriotic than you who knows or is willing to learn what it takes to finish the job, and school is not going to get in the way.
Added: Engineering is a practice, not an immutable identity. Even if you publicly shame all the "engineers" away from contributing to an effort you disagree with, replacing them is a matter of learning enough of the practice to complete the task. Even if we were just talking about what is in paper books today, it's hard to say that anyone could have control over who is or isn't capable of engineering efforts.