Try it the other way:
var start_date = $("#fit_start_time").val(); //05-09-2013
var end_date = $("#fit_end_time").val(); //10-09-2013
var format='dd-MM-y';
var result= compareDates(start_date,format,end_date,format);
if(result==1)/// end date is less than start date
{
alert('End date should be greater than Start date');
}
OR:
if(new Date(start_date) >= new Date(end_date))
{
alert('End date should be greater than Start date');
}