In the STAR WARS movies (at least the original trilogy) no one calls the Imperial fighters "twin ion engine" fighters. They say "T.I.E. fighters," which lets them off the hook. It is only in the "making of" and fan books that "twin ion engine" comes out. Science fiction can get away with any techno-babble, so long as it does not misuse established terminology—such as having an FTL starship engineer gush over a very slow, low thrust engine, or repeatedly use the term "galaxy" in place of "solar system," as in LOST IN SPACE. (Or having Uhura pick up AM broadcasts from orbit in "A Piece of the Action.")
Attempting to rationalize "ion" as an acronym in the case of "Spock's Brain" is attempting to hold back the tide with a fork. The episode is a complete train wreck—perhaps a funny train wreck, depending on one's sense of humor.
"The Doomsday Machine" used a non-committal bit of techno-babble by giving the DM a "total conversion drive." And "Obsession" gave The Creature gravity propulsion. (Tom van Flandern's Meta Model, partly derived from LeSage's corpuscular gravity, puts gravity on the order of 20 billion
times faster than light.) One should really be wondering why an entity of that sort has a taste for hemoglobin...
The point is, an ion engine is not some aspect of the universe that may be wrongly interpreted by contemporary physics. It is an established bit of engineering. Having sci-fi characters punch a hole through an armored steel wall with hand-thrown tennis balls would be equally ridiculous.