Any sensible commander wouldn't pit troops who've just "defected" against their own people would they? They'd only be as loyal as Merc units, besides your own factions generals have a tendancy to be disloyal and you have to account for that don't you?

It just seems a waste to kill off 3,000 troops (i.e. a full stack) with just one click of a mouse when I could.......

.....march them to the coast, board a fleet, ship them to the otherside of Europe, capture another city then disband them into Loyal subjects - all for NO cost to my treasury apart from the upkeep of perhaps 5 turns.