The array you use to set the 'Data' property of the datagrid would usually be a cell array.
When the callback is executed the values in the array will reflect the current state of the checkboxes. That is, you don't need to set them.
If you do want to set table_data, you should use something like:
table_data{row,column} = eventdata.NewData;
BTW, I'm assuming you have set the column format to "Logical" in Guides Table Property Editor.