Case in point, as throwing a [monkey] wrench into the central story-telling engine as you put it is precisely what the allegory demands, not to mention that presenting obstacles for the characters to overcome, including choices between multiple bad alternatives, is a good thing in drama. Delete, reset, ignore is of course the opposite of good drama as are magic plot transition devices such as warp drive and transporters*, and Trek is guilty of these on many occasions, including here.**
* - Range and shield status are swept aside for transporter use, whenever the plot demands.
** - As this is off-topic, now, really, this is all I'm going to say in this thread about whether "Force of Nature" is a mediocre episode; carry on.