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Try to prevent the default behaviour of the click event using jQuery right from the beginning:

jQuery(function ($) {

var $container = $('#isotope-list'); //The ID for the list with all the 
blog posts
var $isotope = $container.isotope({ //Isotope options, 'item' matches the class in the 
PHP
itemSelector : '.item', 
layoutMode : 'masonry'
});

//Add the class selected to the item that is clicked, and remove from 
the others
var $optionSets = $('#filters'),
$optionLinks = $optionSets.find('a');

$optionLinks.click(function(e){
e.preventDefault();
var $this = $(this);
// don't proceed if already selected
if ( $this.hasClass('selected') ) {
return false;
}
var $optionSet = $this.parents('#filters');
$optionSets.find('.selected').removeClass('selected');
$this.addClass('selected');

//When an item is clicked, sort the items.
var selector = $(this).attr('data-filter');
$isotope.isotope({ filter: selector });

return false;
});

});