The problem is, Space Seed and WNMHGB were stellar, memorable episodes and TWOK is still a perfect movie. It doesn't make sense to compete with those - and make no mistake, they will be compared if that is the case.
I prefer to see the Star Trek mythos expanded upon. I'd rather have a new villain to hate than a different reason to hate Khan.
By that logic should the Dark Knight have not used the Joker since Batman '89 was the only good Burton film?
Should TUC not have had Klingons since they had been used in many episodes and movies beforehand.
Now I personally don't think that Khan shows up in the movie. And if he did I wouldn't want him wandering around under an assumed identity without a really good reason, but I would have no problems at all if Khan did show up in the new timeline.