I agree with you…to a point. Story should come first, but if a story fails the Blechdel Test, there should be a good, defensible reason for it, and there are good reasons to fail the test, e.g. a story takes place exclusively on a Royal Navy ship circa 1800; there were no women there, so it wouldn’t make sense to pass. I’ll buy it.
In Star Trek though, there are fewer defensible reasons because of the nature of the show. Off the top of my head, “Measure of a Man” could have Capt. Louvois discussing Android rights with Dr. Pulaski (without mentioning Data) or Troi expressing to Guinan how upsetting it is that these trials are necessary. Does the lack of a scene like that make the episode bad? No. It starts a discussion, though, which is the primary purpose of the test to begin with. In the case of “Measure of a Man,” a scene like that would have probably been left on the cutting room floor to make way for a tighter story that just happened to not have women at the center of it.
Also, reasonable people can disagree on how important a particular scene could be, but the discussion of female representation is still an important one. The goal isn’t to “pass” the test for everything, but there shouldn’t be an overwhelming amount of failures of the test.