This is a serious problem in the military today. One of the things that was especially annoying were the prayer breakfasts that every commander basically had to attend if the brigade commander was an evangelical Christian. It is quite sad that the Chaplain Corps does not mirror the makeup of the military today.
I also think it is awful that many mainline Protestant and Roman Catholic leaders don't encourage their clergy to join the military. Barring the military from seminaries is awful, just as barring ROTC from universities has been awful; all it does is lower the quality of the Officer Corps and lead to the further detachment of the military from general society.