More like everyone starts as a rookie but in the game you can have say for example 6 officers per base. So 6 of your rookies can be aligned to the command tree and become lieutenants, and the rest get aligned to the combat tree and become privates.
In the real military Enlisted don't often become officers, it does happen but officers are usually commissioned from college graduates and those who have attended some form of military academy.
Maybe even flesh out the stats of individual characters so that those with certain attributes make better commanders and other attributes make better soldiers.
In short Give the player choices, and make those choices matter.
Maybe a better title for the characters that aren't specialized is recruit, rather than rookie.