Quick hack to remove a specific category from the Filter Bar (3.9) output

remove-category-filter-categories.php

/**
 * You could add this snippet to your theme's functions.php file
 * or any other suitable location.
 */
add_filter( 'tribe_events_filter_values', 'filter_categories_in_category_filter', 10, 2 );

/**
 * Handles modifying the list of event categories within Filter Bar.
 * 
 * @param  $values
 * @param  $filter_slug
 * @return mixed
 */
function filter_categories_in_category_filter( $values, $filter_slug ) {
	// For any other filter, return the value list unmodified
	if ( 'eventcategory' !== $filter_slug ) return $values;
	
	// This is the *name* of the category we wish to remove
	$to_remove = 'Jolly Japes and Adventures';

	// Find and remove the category if it exists: this could be extended for
	// better handling of parent/child categories if needed
	foreach ( $values as $index => $item )
		if ( $to_remove === $item['name'] ) unset( $values[$index] );
	
	// Return our modified list
	return $values;
}