There has been some recent talk that the morale bonus isn't necessarily something that is retained with each discrete unit created within a settlement but applied as a per-battle bonus to the owning factions' forces defending a settlement only. If true, this means that a temple in Roma that gives a +3 morale bonus would only do so to any defending units in the city of Roma if there was an external attack.

Maybe we're talking about the same thread here - I don't remember where I saw the original post related to this.