What happened to Miss Gulch?

It's true that the movie is silent on the fate of Miss Almira Gulch. Even the original shooting script, which contains a lot of material excised from the final edit, never reveals whether or not she survived the twister. On the face of it, her survival would appear to put a damper on the whole story: presumably she would show up sooner or later with the same sheriff's order and attempt to take Toto away to be destroyed.

However, there are a number of clues in the movie that suggest that Dorothy's experiences in Oz have equipped her to stand up to and defeat Miss Gulch. At the beginning of the movie this is foreshadowed in Dorothy's conversations with the farmhands Zeke and Hunk, whose counterparts in Oz are the Lion and the Scarecrow:

Dorothy: Zeke, what am I going to do about Miss Gulch? Just because Toto chases her old cat—

Zeke: Listen, honey, I got them hogs to get in.

Hunk: Now lookit, Dorothy, you ain't using your head about Miss Gulch. Think you didn't have brains at all.

Dorothy: I have so got brains.

Hunk: Well, why don't you use them?

Zeke: Listen, kid, are you going to let that old Gulch heifer try and buffalo you? She ain't nothing to be afraid of. Have a little courage, that's all.

Dorothy: I'm not afraid of her.

Zeke: Then the next time she squawks, walk right up to her and spit in her eye. That's what I'd do!

However, Dorothy doesn't follow their advice. When Miss Gulch arrives to confiscate and destroy Toto, Dorothy's handling of the situation shows neither wisdom nor bravery: she only offers to be punished instead ("You can send me to bed without supper!") which obviously won't placate Miss Gulch, and then breaks down in tears, offering no real resistance. Faced with the prospect of an expensive lawsuit ("If you don't hand over that dog, I'll bring a damage suit that'll take your whole farm!"), the Gales acquiesce to Miss Gulch's demands. Even after Toto escapes and returns to Dorothy, the only thing she can think of to keep him safe from Miss Gulch is to run away from home with him, which is both cowardly and unwise.

When Dorothy travels to Oz, she learns from the Scarecrow and the Lion the true meaning of intelligence and courage. And while Dorothy doesn't exercise these virtues herself when she defeats the Wicked Witch of the West (quite by accident), the experience does teach her that even someone as seemingly powerful as the Witch can have a profound and easily exploitable weakness.

It's therefore reasonable to assume that, on her return to Kansas, Dorothy now has both the means and the confidence to stand up to Miss Gulch, should she ever return to confiscate Toto. Perhaps instead of handing over the dog as a sobbing wreck, this time she will stand her ground, hoping to call Miss Gulch's bluff. Or if Miss Gulch wasn't bluffing about the lawsuit, Dorothy might use her brains to appeal to the sheriff, or convince Auntie Em and Uncle Henry to take the matter to trial. In any case, she will almost certainly find and exploit some weakness of Miss Gulch's that will allow her and Toto to emerge victorious.