A soldier who shoot a civilian who's being used as human shield is still held responsible/liable for shooting a civilian.
There's a reason why the enemies taking hostages can stall a military operation for a long time.
I'm not sure about the rest of your post, but this part I agree with at 100%, and I think it is very important to underline it and explain it to the players if they don't get it.
A PC's alignment shifting toward evil isn't a punishment, nor is a PC's alignment shifting toward good a reward.
Alignments in 5e are descriptors for typical behavior, so a shift is just the description staying accurate to the shift in behavior or becoming more accurate.