I thought of that one, too, but I decided not to count it since, if I recall correctly, Wegener didn't actually have a
theory -- he just noticed that the shapes of the continents were suggestive of a past super continent, but proposed no mechanism to explain how the continents could have separated (at least no correct one). Without a plausible mechanism, as you say, the rejection of Wegener's idea was not unreasonable.
But maybe you're right -- it should count as a counter example. But in the spirit of this analogy, maybe the IDistas will come up with a
theory that can be used to definitely identify intelligent design, and we can sit back and have our paradigms shift!