Thomas Ford state that Joseph and Hyrum were under his sworn protection and surrendered as prisoners.
"History, 1838–1856, volume F-1 [1 May 1844–8 August 1844]," p. 269, The Joseph Smith Papers website, accessed September 22, 2021
The Smiths, Joseph and Hyrum, have been ass<ass>inated in jail, by whom it is not known, but will be ascertained. I pledged myself for their safety, and upon the assurance of that pledge, they surrendered as prisoners. The Mormons surrendered the public arms in their possession, and the Nauvoo Legion submitted to the command of Capt. Singleton, of— Brown county, deputed for that purpose by me. All these things were required to satisfy the old citizens of Hancock that the Mormons were peaceably disposed, and to allay jealousy and excitement in their minds. It appears however that the compliance of the Mormons with every requisition made upon them, failed of that purpose. The pledge of security to the Smiths was not given upon my individual responsibility. Before I gave it, I obtained a pledge of honor by a unanimous vote from the officers and men under my command, to sustain me in performing it. If the assassination of the Smiths was committed by any portion of these, they have added treachery to murder, and have done all they could to disgrace the State, and sully the public honor.
It's unclear whether "The Mormons" who Thomas Ford refers to here who surrendered their weapons includes Joseph and Hyrum along with the Nauvoo legion or not.