I think they will have the good sense to use characters from 'good' episodes.
Sometime before the movie opens the villain's name will get out.
The media and casual fans upon finding the name would look at that episode and go "oh god that's a terrible episode!"
That's why they'll never use Garth in a movie. Cool concept--the Starfleet's greatest captain gone insane and on a violent rampage.
And then people look at 'Whom Gods Destroy' with all the overacting and nonsense and ridicule it. Not good publicity.
No offense, but I don't remember Space Seed
being all that highly regarded prior to The Wrath of Khan
Whether the villain comes from a good or bad episode isn't going to matter to general audiences who don't follow Trek.