The ruler wouldn't have direct control of the army, but he would have authority over his General(s). You will say, yeah, he already has that, but that is poorly defined and not really enforced - the only time a ruler would now override his Generals orders is if they were suicidal - and that is a big IF, too.
This feature is really focused on changing, or better to say defining more clearly the role of a ruler and a General(s). The current system is usually misunderstood and is not being played as it should be. There was a huge topic few weeks back where it was clear that rarely anyone plays the role of a General according to the guidance provided on the BM Wiki.
So, your priest ruler of your theocracy wouldn't say to his Generals when to refit, what settings to use when attacking and stuff like that, but he would say go forth and take back our holy city for our faith.
What I am saying is that this can be achieved if the same character is both ruler and general, which is a perfectly legit thing to do. Basically your proposal would remove a possibility, but would in fact not add any, as it is already possible to do it.
