It's suspiciously difficult to tell from the evidence whether Fanny and Joseph were married; which makes it feel suspicious, IMHO. If it wasn't marriage, it is highly likely that Joseph Smith and the rest of the Church would've referred it to marriage after the fact. The lack of record and lack of details also feels suspicious to me. Here's my list:
In favor of the marriage:
1. Fanny's mother testified that a "sealing" of sorts happened.
I do not know that the “sealing” commenced in Kirtland but I am
perfectly satisfied that something similar commenced, and my judgment is
principally formed from what Fanny Alger told me herself concerning her
reasons for leaving “Sister Emma.
2. Mosiah Hancock recorded in the 1890s that Joseph had approached Fanny's father to ask for her hand in marriage.
Samuel, the Prophet Joseph loves your daughter Fanny and wishes her for a wife. What say you?” Uncle Sam says, “Go and talk to the old woman [Levi’s sister and Fanny’s mother] about it. Twill be as she says.” Father goes to his sister and said, “Clarissy, Brother Joseph the Prophet of the most high God loves Fanny and wishes her for a wife. What say you?” Said she, “Go and talk to Fanny. It will be all right with me.” Father goes to Fanny and said, “Fanny, Brother Joseph the Prophet loves you and wishes you for a wife. Will you be his wife?” “I will Levi,” said she. Father takes Fanny to Joseph and said, “Brother Joseph I have been successful in my mission.” Father gave her to Joseph, repeating the ceremony as Joseph repeated to him.
However, this seems to conflict with Fanny's mother's record above.
3. William McLellin did refer to the act Emma caught JS and Fanny in as a "sealing", which took place on the hay.
4. Joseph Smith did state in 1835,
The Lord God of Israel has given me authority to unite the people in the holy bonds of matrimony. And from this time forth I shall use that privilege and marry whomsoever I see fit.
However, this was more than a year before the sealing power was restored. Fanny did leave within a few months after the sealing powered was restored, but it seems much of the "incident" happened before then.
1. Five years apart for the revelation and the rest of the wives.
2. After JS death, William McLellin wrote to JS III
Emma saw him, and spoke to him. He desisted, but Mrs. Smith refused to be satisfied. He called in Dr. Williams, O. Cowdery, and S. Rigdon to reconcile Emma. But she told them just as the circumstances took place. He found he was caught. He confessed humbly, and begged forgiveness. Emma and all forgave him. She told me this story was true!! Again I told her I heard that one night she missed Joseph and Fanny Alger. She went to the barn and saw him and Fanny in the barn together alone. She looked through a crack and saw the transaction!!! She told me this story too was verily true.
However, Joseph Smith III and his mother Emma went on denying that JS ever practiced or preached polygammy. William McLellin was also excommunicated twice; the first time for adultery, the reinstated and ordained an apostle, and then excommunicated again for apostasy.
3. Martin Harris' record
In or about the year 1833, the servant girl of Joe Smith stated that
the prophet had made improper proposals to her, which created quite a talk
amongst the people. Joe Smith went to Martin Harris to counsel with him
concerning the girl’s talk. Harris, supposing that Joe was innocent, told him to
take no notice of the girl, that she was full of the devil and wanted to destroy
the prophet of God; but Joe Smith acknowledged that there was more truth
than poetry in what the girl said. Harris then said he would have nothing to
do in the matter, Smith could get out of the trouble the best way he knew how.
4. After Fanny left Kirtland, Joseph Asked her uncle Hancock to take her to Missouri, but she ran off with her parrents instead. She wound up in Indiana, where she married Solomon Custer, who wasn't mormon. She also suspiciously married him only a couple of weeks after they had met...
5.After JS' death, she was asked what her relationship was with the prophet. She replied, "That is a matter of my own. And I have nothing to communicate."
6. Oliver Cowdreywas also excommunicated for the accusation that Joseph Smith had committed adultery with Fanny. Had it been a polygamous marriage, the Church council would've acknowledged it.
7. The official doctrine of polygammy wasn't issued until 1843. Its earlier practice was shrouded in secrecy.