Yah, the sandpeople holding Shmi Skywalker as a prisoner doesn't really make sense SW universe wise. It seems to solely be that way because it was needed for story purposes, so there could be that good-bye scene as the cause for Anakin's loss of control.

The explanation I have tinkered around this 'scripted sequence' is rather bland and simple: The Tusken Raiders are Tattooine's native people and the relations between them and the outworld colonists is similar to the animosities between the native americans and the british settlers. A classic Wild West scenario, so to speak. They simply wanted to slowly torture her to death and take her scalp, because the 'white man' had driven them from their land.

Perhaps this story will be told in one of the upcoming prequel era EU books.