It already sucked in Civ 1 and it took many iterations (i think some patch Civ 4) to stop.
All of the Civilization games had tile management. Fallen Enchantress has no tile management economics - there is no turn-by-turn action that the player can take to change the amount of production in a city. (Edit: The exception to this is changing city enchantments - but that spends another resource, mana, to gain a tiny amount of production efficiency).
If you can't increase or decrease production turn-by-turn, there is no need to worry about production overrun. In Civilization, the player would have a small incentive to change production to trade / food temporarily then change it back. Fallen Enchantress does not have such an impetus, so from the city production management standpoint overrun is irrelevant.
The point about the gold is valid, as that will push the city to the next item in the production queue, speeding it up by a turn. A simple fix here could be for rush-buying to merely "fill up" the production gauge, allowing the queued item to complete at the start of the subsequent turn. However, this would remove the immediate benefit of the "instant completion." This immediate-reward system is one of the primary needs for games to continue to be fun, running off a similar concept to the chime or ring or spin that a gambler gets when playing a slot machine.
Perhaps a scripted placeholder "building" could be placed into the queue after rush-buying. This "temporary" rush-buy construction could be called [Completing Purchased Infrastructure] or [Finishing Hurried Unit] and would last until the end of the turn before disappearing. The player would be able to move around the rest of the queue, but not this initial item.