it was a practise, but it WASN'T commonly practised if you know what i mean. It was entirely up to the generals discretion and could be for any offense as far as i'm aware not just an army who ran from the field. It was i believe fairly controversial even back then, not that anyone would gainsay a general who wished to do it but it wasn't considered the ideal way to deal with a deserting army.
I think Crassus was famous for doing it to the legions he received to fight spartacus. The legions in question had actually broken a couple of times when facing spartacus's armies and crassus decimated them as one of his first orders of buisness when he took charge.
I think it wouldn't be bad as an option, perhaps available to do anytime rather than alwasy after a defeat. It could give like plus 2 morale for the next battle or something. Though i think it wasn't a common enough practise for me to be overly concerned if it's not included.