The DataGridView does not support individual Cell hiding, only whole columns.
Probably the most simiple way you have got is to activate the Panel of the cell and have it span one column and one row, which means it will overlay this one particular cell. Every cell in a DataGridView has a Panel associated with it (DataGridViewCellPanel) which is hidden by default. If you need/want you can add what ever control you want to this panel, but in this case it may be sufficient to just show it in order to hide the checkbox.
To enable/show a panel for a specific cell you can use the following code:
this.dataGridView1.Rows.Cells.Panel.Rowspan = 1;
this.dataGridView1.Rows.Cells.Panel.Colspan = 1;
You also have the option of creating custom column types, in which case you might be able to have a UserControl as the contents of the cell. See more information in this CompanionKit's sample here.
Hope this helps,