"If, on the other hand, babies near me are being murdered by those working for God, just following orders, then my actions may not actually help them do God's good work."
I think that you can be safe in saying that. I also will not accept any so called "spiritual" leading to murder any babies nor help in the effort to do so.
That was then, this is now.
I will not however, question God or his command as documented in the historical and supernatural record called the Holy Bible. I do not understand everything. I question lots of things, but not God's Word. We have a written record of what was then. What is now is that we are commanded to love one another. If we could but acheive that one thing, there would be no drones. But just like omniscience is impossible as a mortal, so is perfect love; even among those that Name the Name of Christ whether it be falsely or in truth.
The most important thing for you to know is that God loves you, Joe, and that His Son, God Himself, the Lord Jesus Christ, has provided a way for you to stand before Him in righteousness, which is impossible humanly.