There are a goodly number of sacred troops in Dom II. I'd be worried it would tip things out of balance if any troop could become sacred. What would the point be to Marignon's fragile flagellants then, for example?
I think it would also make god design too much of a blessing-engineering event as well. As it is, I think the balance is right between trying to get the right magic power, the blessings you'd like, and sparing points for a good strong dominion and the fortress type you want. Being able to sanctify troops would tip more importance towards blessing power during god design, and that would devalue other equally-interesting paths.
(Oh, and speaking of the random flagellant event, it happens a lot now. I get more of the little weirdoes than I care for, honestly.
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