I used to expect to lose a significant number of Leaders during any average to large sized scenario. I wouldn't normally lose anything above Brigade level commanders but I would still lose enough of them to see a significant drop in the integrity of my Army command bonuses.
Playing in ignorance despite my experience it just becomes an accepted trial to see your Leaders being skittled away as the turns progress.
In fact it was in a multi-player game against a Reb team that included Generals Kennon & Ross McDaniel that I had my belated light-bulb moment
Ross made some comments regarding my (teams) poor Leader handling and I went away to ponder the lesson and actually sit and read the manual properly.
I can say that since that moment my Leader casualties have been limited to a few unfortunates in what has become a vey rare occurrence.
The proof in the testing of my new doctrine came when I subsequently held Kennon to a draw on the first day at 2nd Bull Run ...in large part because I was able to drag the utmost out of my Leader command modifiers.