I would use codebehind:
protected void OnCheckboxListItemBound(Object sender, RepeaterItemEventArgs e)
{
if (e.Item.ItemType == ListItemType.Item || e.Item.ItemType == ListItemType.AlternatingItem)
{
HtmlTableRow itemRow = (HtmlTableRow) e.Item.FindControl("itemRow");
itemRow.Visible = e.Item.ItemIndex % 2 == 0;
}
}