Well, just because the Temporal Cold War plot wasn't B&B's idea originally doesn't mean they didn't have at least some
thing in mind for an eventual pay-off. Sure, there never were any serious plans to conclude that storyline, but I don't think that has to mean Braga didn't have at least a hint of an idea in the back of his head.
I still think he could be serious and that a story actually showing this development could have been satisfactory. If done well, of course.