Tom is not going to marry Myrtle. At least this is an inference available to us given Tom's history. He has had affairs before - and been caught - yet he has not communicated a real interest in divorcing Daisy. His affairs are simply affairs.
Daisy does not follow this pattern of behavior. She is courted by a man who clearly wants to marry her. Gatsby is not merely making overtures of affection. His intentions are clear. Daisy understands this. Her affair then has the potential to break up the marriage.
Though this difference is "only" a difference in attitude and degree, it is an important difference between these two affairs.
Additional differences include the fact that Tom and Myrtle are not part of the same social/financial class. While Gatsby was not born rich, he is now wealthy and capable of providing for Daisy's material needs. The class difference is not the same for Daisy as it is for Tom and Myrtle.