When plots defy me

Plenty of writers have anecdotes about how this or that character suddenly “came to life” and took over the story. I’ve often felt the same about plots, or stories as a whole: They have their own path and it’s mostly a matter of me stumbling on it and working out where we’re going.
The trouble is, sometimes I don’t like where we’re going. Not in the way that Affairs of Honor ends on a more downbeat note than I’d like (as I noted last week), but where the story has changed to the point it’s no longer interesting.
This occurred to me today while working on Never Call Up What You Cannot Put Down. My original interest was sparked by David Clarke’s book Angel of Mons. I began thinking hmm, what if the WW I legend was true? And Arthur Machen’s story (the supposed inspiration for the myth) were part of a British government cover up? (It’s the Tim Powers No Coincidence approach I blogged about previously).
As written, working the legend into a WW II story requires a lot of exposition—reasonably well handled, but not well enough to work. So I’ve been de-emphasizing the legend, but I realized today that this doesn’t satisfy me either. Now it’s just one more battle to stop the Nazis accessing a supernatural talisman, and lord knows, we’ve seen that often enough.
One option is just to give up. Or throw it into my beta file and check back on it some time in the future (might be a while. Beta stories rarely move up to the A-list).
Another is to really, really rework it. Find a plot that places the Angel front and center without drowning the reader in exposition and doesn’t feel too old hat.
I have a variation of the problem with Fiddler’s Black. It started out as a light romantic fantasy about a woman fascinated by the musician living next door to her. Now it’s turned into something very dark, which I wouldn’t object to, except I’m not sure I can pull it off. So do I try and pull it off? Or work my way back light and charming?
Once again, we will have to see.