Using jQuery you can easily remove the checkbox. ASP.NET Gridview generating mark up as HTML table in the browser. By using that html table id you can loop through all rows and cols like below using jquery.
$('table#yourTable tr').each(function(){
var isEmpty = true;
$(this).children('td').each(function(){
if($.trim($(this).html()) == '') {
$('input:checkbox').remove();
}
});
});