I think the Elton's choose Jane over Emma because Emma rebuffed Mrs. Elton's attempts at familiarity. Had Emma been more receptive to musical clubs and taking Jane under their collective wings she would not have an enemy in the Eltons. I think Mrs. Elton is too much of a society hound to hold a grudge if they had become patronesses together:

In one respect Mrs. Elton grew even worse than she had appeared at first. Her feelings altered towards Emma. Offended, probably, by the little encouragement which her proposals of intimacy met with, she drew back in her turn and gradually became much more cold and distant; and though the effect was agreeable, the ill-will which produced it was necessarily increasing Emma's dislike. Her manners too -- and Mr. Elton's, were unpleasant towards Harriet. (33)

Emma and Mrs. Elton’s tête-à-tête in Ch. 32 reminds me of Emma and Jane’s tête-à-tête in Ch. 20 only this time it is Emma who is cool, polite and reserved and it is Mrs. Elton who is materially offended. Emma accepted Mr. Knightley’s heart in Ch. 49 and I can’t help but wonder if the Elton’s will change their behavior towards if Emma if she becomes the elusive Mrs. Knightley.