Hi P.,
First, thank you for your sacrifice and for your husbands valiant service. It is incredibly humbling to know he is there for our greater freedom, and our childrens.
As a little bit older mom, I now ask myself the question of what is the long term results of both disciplines? If he is in a room, scared and alone, and finally sleeps, what will that do? Will it leave him feeling protected by his mom or will it leave him feeling like he is alone and unprotected. What will the teen and young adult reaction to that feeling be?
If you keep him up until he is much more tired and can fall asleep faster with you with him, what is the long term of that? Perhaps you could add a nap in as well until he gets through the fear.
There are many options, which I know you have a load on you, but think about what you can do to accomodate his fear and make sure he knows Mom will be there - even when times are very hard. He will know he can count on you to help him find a solution. No, you don't have to fully accomodate his every whine, but at three, he does need you to be his protector. I would bet the next storm will be worse if you let him scream it out and then you will have to let him scream it out for longer. Be sensitive to that fear and wrap your arms around him at the sight of a lighting bolt. He will begin to feel warm and a bit silly everytime you hug him tight at the sound of something that does not even bother him. When he is older, he will say, gosh, mom just wanted to hug me everytime it stormed - I bet she was scared. Wow-what a difference from - Noone cares when I am scared, I am all alone and must protect myself. What will those walls do for his relationships?
Another idea would be to put him on the couch instead of his room as you move around. It would surely be short lived as he probably won't sleep, but allow him a wind down with all the lights dim until he is really tired.
I am sure you are a fabulous mom and either way you choose, you will find a way to ensure him that you are there, and you care.
Best of luck, J.