How does Army decide on who to discipline and who not to?

It stems from the UCMJ itself. If you look at the punishments for enlisted compared to punishments for officers you will see that the enlist face stiffer penalties for violations.

I recall a friend who was a soldier who had an adulterous affair. I also recall his wife who questioned the Army's punishment protocols. How is it that the soldier gets fined, loses a stripe and either restriction or brig time, but yet it's the family that suffers twice. First from the affair and then the screwing from the Army??? I suppose I get the basic premise, make the punishment so severe no one will do it, just like capital punishment was designed to keep people from killing other people......

These are the kinds of people that ruin it for all of us.